Transition-metal complexes of group 12 with 1,1′-bis(phosphanyl)ferrocene ligands

The syntheses of four new cadmium and zinc complexes with 1,1′-bis(phosphanyl)ferrocene ligands and their phosphine chalcogenide derivatives are reported. The complexes were characterized by elemental analyses and IR, 1H NMR, 31P NMR and electronic absorption spectroscopy. The crystal structures of dichlorido[1-diphenylphosphinoyl-1′-(di-tert-butylphosphanyl)ferrocene-κ2 O,P]cadmium(II), [CdCl2{(C17H14OP)(C13H22P)Fe}] or CdCl2(κ2 P,O-dppOdtbpf) (1), bis[μ-(tert-butyl)(1′-diphenylphosphinoylferrocen-1-yl)phosphinato-κ3 O,O′:O′′]bis[chloridozinc(II)], [Zn2{(C9H13O2P)(C17H14OP)Fe}2Cl2] or [ZnOCl{κ2 O,O′-Ph2POFcPO2(t-Bu)}]2 (2), 1,1′-bis(di-tert-butylthiophosphinoyl)ferrocene, [Fe(C13H22PS)2] or dtbpfS2 (3), and [1,1′-bis(dicyclohexylphosphanyl)ferrocene-κ2 P,P′][chlorido/cyanido(0.25/1.75)]zinc(II), [Zn(CN)1.75Cl0.25{(C17H26P)2Fe}] or Zn(CN)2(κ2-dcpf) (4), were determined crystallographically. Compound 1 has tetrahedral geometry in which the CdII centre is coordinated by one dppOdtbpf ligand in a κ2-manner and by two Cl atoms, while compound 2 displays a centrosymmetric dimeric unit in which two oxide atoms bridge the two Zn atoms to generate an eight-membered ring. Compound 3 revealed a sandwich structure with both phosphane groups sulfurized. In compound 4, the ZnII atom adopts a tetrahedral geometry by coordinating to the 1,1′-bis(dicyclohexylphosphanyl)ferrocene ligand in a κ2-manner and to two cyanide ligands.

Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics

ABSTRACTCoronavirus (CoV) non-structural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase (RdRp) and other nsps. To date, no structure of full-length SARS-CoV-2 nsp7:nsp8 complex has been published. Current understanding of this complex is based on structures from truncated constructs or with missing electron densities and complexes from related CoV species with which SARS-CoV-2 nsp7 and nsp8 share upwards of 90% sequence identity. Despite available structures being solved using crystallography and cryo-EM representing detailed snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the complex and how it assembles to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the structural dynamics of the SARS-CoV-2 full-length nsp7:nsp8 complex. The results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without altering nsp7-nsp8 interactions.

Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands

Inositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

Acrylamide Fragment Inhibitors that Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and SARS-CoV-2 Main Protease

ABSTRACTRNA viruses are critically dependent upon virally encoded proteases that cleave the viral polyproteins into functional mature proteins. Many of these proteases are structurally conserved with an essential catalytic cysteine and this offers the opportunity to irreversibly inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that selectively target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we effectively re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold as well as similar catalytic-triad. We demonstrate that the hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. In addition, we provide the first demonstration that targeting the active site cysteine of Mpro can also have profound allosteric effects, distorting secondary structures required for formation of the active dimeric unit of Mpro. These new data provide novel mechanistic insights into the design of EV71 3Cpro and SARS-CoV-2 Mpro inhibitors and identify acrylamide-tagged pharmacophores for elaboration into more selective agents of therapeutic potential.

Crystal structures of two dysprosium–aluminium–sodium [3.3.1] metallacryptates that form two-dimensional sheets

The two [3.3.1] metallacryptate complexes, namely, poly[[μ3-acetato-hexakis(μ-N,N-dimethylformamide)bis(N,N-dimethylformamide)bis[salicylhydroximato(2−)]heptakis[salicylhydroximato(3−)]hexaaluminium(III)dysprosium(III)pentasodium(I)] N,N-dimethylformamide tetrasolvate monohydrate], [DyAl6Na5(OAc)(Hshi)2(shi)7(DMF)8]·4DMF·H2O or {[DyAl6Na5(C7H5NO3)2(C7H4NO3)7(C2H3O2)(C3H7NO)8]·4C3H7NO·H2O} n , 1, and poly[[di-μ4-acetato-nonakis(μ-N,N-dimethylformamide)octakis(N,N-dimethylformamide)tetrakis[salicylhydroximato(2-)]tetradecakis[salicylhydroximato(3−)]dodecaaluminium(III)didysprosium(III)decasodium(I)] N,N-dimethylformamide 6.335-solvate], [DyAl6Na5(OAc)(Hshi)2(shi)7(DMF)8.5]2·6.335DMF or {[Dy2Al12Na10(C7H5NO3)4(C7H4NO3)14(C2H3O2)2(C3H7NO)17]·6.335C3H7NO} n , 2, where shi3− is salicylhydroximate and DMF is N,N-dimethylformamide, both consist of an aluminium-based metallacryptand. In 1 and 2, the metallacryptand encapsulates a dysprosium(III) ion in the central cavity, and the resulting metallacryptates are connected to each other via sodium-DMF linkages to generate a two-dimensional sheet. The metallacryptates of 1 and 2 are the three-dimensional analogues of metallacrowns as the metallacryptates contain a metal–nitrogen–oxygen cyclic repeat unit throughout the complexes. For 1 the building block of the two-dimensional sheet is comprised of only one type of metallacryptate, which is connected to four neighboring metallacryptates via four sodium–DMF linkages. In 2, the building block is a dimeric unit of two metallacryptates. Each dimeric metallacryptate unit is connected to four other dimeric units via six sodium–DMF linkages. The two metallacryptates of each dimeric unit can be considered enantiomers of each other. In both 1 and 2, chirality is imparted to the metallacryptate due to the Λ and Δ propeller configurations of the four octahedral aluminium ions of the metallacryptand shell.

Dinuclear Copper(II) Complexes with Schiff Bases Derived from 2-Hydroxy-5-Methylisophthalaldehyde and Histamine or 2-(2-Aminoethyl)pyridine and Their Application as Magnetic and Fluorescent Materials in Thin Film Deposition

Two Cu(II) complexes, 1 and 2, with tridentate Schiff bases derived from 2-hydroxy-5-methylisophthalaldehyde and histamine HL1 or 2-(2-aminoethyl)pyridine HL2, respectively, were obtained and characterized by X-ray crystallography, spectroscopic (UV-vis, fluorescence, IR, and EPR), magnetic, and thermal methods. Despite the fact that the chelate formed by the NNO ligand donors (C26-C25H2-C24H2-N23=C23H-C22-C19Ph(O1)-C2(Ph)-C3H=N3-C4H2-C5H2-C6 fragment) are identical, as well as the synthesis of Cu(II) complexes (Cu:L = 2:1 molar ratio) was performed in the same manner, the structures of the complexes differ significantly. The complex 1, {[Cu2(L1)Cl2]2[CuCl4]}·2MeCN·2H2O, consists of [Cu2(L1)Cl2]+ units in which Cu(II) ions are bridged by the HL1 ligand oxygen and each of these Cu(II) ions is connected with Cu(II) ions of the next dimeric unit via two bridging Cl− ions to form a chain structure. In the dinuclear [Cu2(L2)Cl3]⋅0.5MeCN complex 2, each Cu(II) is asymmetrically bridged by the ligand oxygen and chloride anions, whereas the remaining chloride anions are apically bound to Cu(II) cations. In contrast to the complex 1, the square-pyramidal geometry of the both Cu(II) centers is strongly distorted. The magnetic study revealed that antiferromagnetic interactions in the complex 2 are much stronger than in the complex 1, which was corresponded with magneto-structural examination. Thin layers of the studied Cu(II) complexes were deposited on Si(111) by the spin coating method and studied by scanning electron microscopy (SEM/EDS), atomic force microscopy (AFM), and fluorescence spectroscopy. The Cu(II) complexes and their thin layers exhibited fluorescence between 489–509 nm and 460–464 nm for the compounds and the layers, respectively. Additionally, DFT calculations were performed to explain the structures and electronic spectral properties of the ligands.

Structure of the yeast Nup84-Nup133 complex details flexibility and reveals universal conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus, occurs through the Nuclear Pore Complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex, from one species. The structure of Nup84-Nup1 33CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor (ALPS) motif, confirmed by liposome interaction studies. The new structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

Bismuth⋅⋅⋅π arene interaction in [Bi{OC6H4(CH2C6H5)-2}3]2

We report on the synthesis of a new bismuth aryloxide molecule Bi[OC6H4(CH2C6H5)-2]3 (1), which was characterized by NMR and IR spectroscopy as well as single-crystal X-ray diffraction analysis. A characteristic structural feature is the dimeric unit with a central Bi2O2 core resulting from μ-binding phenolates. In addition, both bismuth atoms show a Bi⋅⋅⋅π arene interaction with a quite short Bi⋅⋅⋅πcentroid distance of 3.11 Å in the solid state.

Crystal structures of binuclear complexes of gadolinium(III) and dysprosium(III) with oxalate bridges and chelating N,N′-bis(2-oxidobenzyl)-N,N′-bis(pyridin-2-ylmethyl)ethylenediamine (bbpen2−)

The reaction between mononuclear [Ln(bbpen)Cl] [Ln = Gd or Dy; H2bbpen = N,N′-bis(2-hydroxybenzyl)-N,N′-bis(pyridin-2-ylmethyl)ethylenediamine, C28H30N4O2] and potassium oxalate monohydrate in water/methanol produced the solvated centrosymmetric isostructural binuclear (μ-oxalato)bis{[N,N′-bis(2-oxidobenzyl-κO)-N,N′-bis(pyridin-2-ylmethyl-κN)ethylenediamine-κ2 N,N′]dilanthanide(III)}–methanol–water (1/4/4) complexes, [Ln 2(C28H28N4O2)2(C2O4)]·4CH3OH·4H2O, with lanthanide(III) = gadolinium(III) (Ln = Gd) and dysprosium(III) (Ln = Dy), in high yields (ca 70%) directly from the reaction mixtures. In both complexes, the lanthanide ion is eight-coordinate and adopts a distorted square-antiprismatic coordination environment. The triclinic (P\overline{1}) unit cell contains one dimeric unit together with four water and four methanol molecules; in the final structural model, two of each type of solvating molecule refine well. In each lanthanide(III) dimeric molecule, the medium-strength O...H—O hydrogen-bonding pattern involves four oxygen atoms, two of them from the phenolate groups that are `bridged' by one water and one methanol molecule. These interactions seem to contribute to the stabilization of the relatively compact shape of the dimer. Electron densities associated with an additional water and methanol molecule were removed with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. These two new compounds are of interest with respect to magnetic properties.