A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.

The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from 10 COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb, CV07-209, neutralized authentic SARS-CoV-2 with an IC50 value of 3.1 ng/mL. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 Å revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2-neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss, and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.

5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.

Drugs frequently require interactions with multiple targets-via a process known as polypharmacology-to achieve their therapeutic actions. Currently, drugs targeting several serotonin receptors, including the 5-HT2C receptor, are useful for treating obesity, drug abuse, and schizophrenia. The competing challenges of developing selective 5-HT2C receptor ligands or creating drugs with a defined polypharmacological profile, especially aimed at G protein-coupled receptors (GPCRs), remain extremely difficult. Here, we solved two structures of the 5-HT2C receptor in complex with the highly promiscuous agonist ergotamine and the 5-HT2A-C receptor-selective inverse agonist ritanserin at resolutions of 3.0 Å and 2.7 Å, respectively. We analyzed their respective binding poses to provide mechanistic insights into their receptor recognition and opposing pharmacological actions. This study investigates the structural basis of polypharmacology at canonical GPCRs and illustrates how understanding characteristic patterns of ligand-receptor interaction and activation may ultimately facilitate drug design at multiple GPCRs.

Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation.

Respiratory syncytial virus (RSV) is a leading cause of infant mortality, and there are currently no licensed vaccines to protect this vulnerable population. A comprehensive understanding of infant antibody responses to natural RSV infection would facilitate vaccine development. Here, we isolated more than 450 RSV fusion glycoprotein (F)-specific antibodies from 7 RSV-infected infants and found that half of the antibodies recognized only two antigenic sites. Antibodies targeting both sites showed convergent sequence features, and structural studies revealed the molecular basis for their recognition of RSV F. A subset of antibodies targeting one of these sites displayed potent neutralizing activity despite lacking somatic mutations, and similar antibodies were detected in RSV-naive B cell repertoires, suggesting that expansion of these B cells in infants may be possible with suitably designed vaccine antigens. Collectively, our results provide fundamental insights into infant antibody responses and a framework for the rational design of age-specific RSV vaccines.

Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.

Transcription factors (TFs) control gene expression by binding DNA recognition sites in genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead (FKH) motif, RYAAAYA, some forkheads recognize a completely different (FHL) motif, GACGC. Bispecific forkhead proteins recognize both motifs, but the molecular basis for bispecific DNA recognition is not understood. We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes. These structures reveal how a single TF binds two unrelated DNA sequences and the importance of DNA shape in the mechanism of bispecific recognition.

Chemical interactions that govern the structures of metals.

Most metals adopt simple structures such as body-centered cubic (BCC), face-centered cubic (FCC), and hexagonal close-packed (HCP) structures in specific groupings across the periodic table, and many undergo transitions to surprisingly complex structures on compression, not expected from conventional free-electron-based theories of metals. First-principles calculations have been able to reproduce many observed structures and transitions, but a unified, predictive theory that underlies this behavior is not yet in hand. Discovered by analyzing the electronic properties of metals in various lattices over a broad range of sizes and geometries, a remarkably simple theory shows that the stability of metal structures is governed by electrons occupying local interstitial orbitals and their strong chemical interactions. The theory provides a basis for understanding and predicting structures in solid compounds and alloys over a broad range of conditions.

Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel.

Influenza virus neuraminidase (NA) is an important target for antiviral development because it plays a crucial role in releasing newly assembled viruses. Two unique influenza-like virus genomes were recently reported in the Wuhan Asiatic toad and Wuhan spiny eel. Their NA genes appear to be highly divergent from all known influenza NAs, raising key questions as to whether the Asiatic toad influenza-like virus NA (tNA) and spiny eel NA (eNA) have canonical NA activities and structures and whether they show sensitivity to NA inhibitors (NAIs). Here, we found that both tNA and eNA have neuraminidase activities. A detailed structural analysis revealed that tNA and eNA present similar overall structures to currently known NAs, with a conserved calcium binding site. Inhibition assays indicated that tNA is resistant to NAIs, while eNA is still sensitive to NAIs. E119 is conserved in canonical NAs. The P119E substitution in tNA can restore sensitivity to NAIs, and, in contrast, the E119P substitution in eNA decreased its sensitivity to NAIs. The structures of NA-inhibitor complexes further provide a detailed insight into NA-inhibitor interactions at the atomic level. Moreover, tNA and eNA have unique N-glycosylation sites compared with canonical NAs. Collectively, the structural features, NA activities, and sensitivities to NAIs suggest that fish- and amphibian-derived influenza-like viruses may circulate in these vertebrates. More attention should be paid to these influenza-like viruses because their NA molecules may play roles in the emergence of NAI resistance.

The Phosphidosilicates AE2 Li4 SiP4 (AE=Ca, Sr, Eu) Ba4 Li16 Si3 P12.

The quaternary phosphidosilicates AE2 Li4 SiP4 (AE=Ca, Sr, Eu) and Ba4 Li16 Si3 P12 were synthesized by heating the elements and Li3 P under argon atmosphere. Their crystal structures were determined by single crystal X-ray diffraction. AE2 Li4 SiP4 crystallize in a new layered structure type (P21 /m, Z=2) with CdI2 -analoguos layers. Edge sharing CaP6 octahedra are separated by layers of vertex-sharing SiP4 and LiP4 tetrahedra, which contain additional chains of LiP6 octahedra. Ba4 Li16 Si3 P12 forms likewise a new structure type (P21 /c, Z=16) with a three-dimensional network of SiP4 , Si2 P6 and LiP4 entities as well as one phosphorus site not bonded to silicon. Barium is located in capped trigonal prisms of phosphorus which form strongly corrugated layers. 31 P and 29 Si solid-state NMR spectra confirm the crystal structures of the compounds AE2 Li4 SiP4 . 7 Li spectra show only one signal in spite of quite different crystallographic positions, which indicate possible Li+ mobility. However, this signal is much broader compared to the known Li+ conducting phosphidosilicates. Accordingly, electrochemical impedance measurements show low Li+ conductivities.

N2H4 derived Sulfonic Acids: Hydrazine Disulfonate, [(SO3)HNNH(SO3)]2-, and Hydrazine Iso-disulfonate, [H2NN(SO3)2]2.

The reaction of hydrazinium sulfate and chlorosulfonic acid in pyridine leads to the pyridinium salt of the hydrazine disulfonate anion, [(SO3)HNNH(SO3)]2-. The salt is the starting material for the preparation of further hydrazine disulfonates, for example of alkaline metals and barium. In all compounds, the [(SO3)HNNH(SO3)]2- anion adopts the gauche conformation. The conformer is chiral but all of the investigated compounds crystallize as racemates. The disulfonate anion can occur in another constitution with the two sulfonate groups attached to only one nitrogen atom. This so-called hydrazine iso-disulfonate, [H2NN(SO3)2]2-, has been prepared through a substitution reaction between potassium imidodisulfonate, K[HN(SO3)2], and hydroxylamine-O-sulfonic acid, H2NOSO3H. The hydrazine iso-disulfonate anion has been crystallized as potassium and barium compound, respectively. The compounds were characterized by XRD, vibrational spectroscopy, DFT calculations and thermal analyses.

The Phase Control of Transition Metallic Elements via Facile Chemical and Physical Syntheses.

The crystal phases of metals are important factors to tune the properties of metals, and therefore received extensive attention. Traditionally, phase control is performed within limited numbers of elements by harsh conditions, such as face-centered cubic Fe by high temperature. This review summarizes most reports in metal phase control area, including elements of Fe, Co, Ni, Cu, Ru, Pd, Rh, Os and Au. For every metallic element, the facile phase control methods are systematically introduced, such as epitaxial growth, ball milling, chemical reduction, etc. Their corresponding applications and the mechanisms for phase control are thoroughly discussed.

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials.

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

Structural and mechanistic insights into the complexes formed by Wolbachia cytoplasmic incompatibility factors.

Wolbachia bacteria, inherited through the female germ line, infect a large fraction of arthropod species. Many Wolbachia strains manipulate host reproduction, most commonly through cytoplasmic incompatibility (CI). CI, a conditional male sterility, results when Wolbachia-infected male insects mate with uninfected females; viability is restored if the female is similarly infected (called "rescue"). CI is used to help control mosquito-borne viruses such as dengue and Zika, but its mechanisms remain unknown. The coexpressed CI factors CifA and CifB form stable complexes in vitro, but the timing and function of this interaction in the insect are unresolved. CifA expression in the female germ line is sufficient for rescue. We report high-resolution structures of a CI-factor complex, CinA-CinB, which utilizes a unique binding mode between the CinA rescue factor and the CinB nuclease; the structures were validated by biochemical and yeast growth analyses. Importantly, transgenic expression in Drosophila of a nonbinding CinA mutant, designed based on the CinA-CinB structure, suggests CinA expressed in females must bind CinB imported by sperm in order to rescue embryonic viability. Binding between cognate factors is conserved in an enzymatically distinct CI system, CidA-CidB, suggesting universal features in Wolbachia CI induction and rescue.

Binding of cardiotonic steroids to Na+,K+-ATPase in the E2P state.

The sodium pump (Na+, K+-ATPase, NKA) is vital for animal cells, as it actively maintains Na+ and K+ electrochemical gradients across the cell membrane. It is a target of cardiotonic steroids (CTSs) such as ouabain and digoxin. As CTSs are almost unique strong inhibitors specific to NKA, a wide range of derivatives has been developed for potential therapeutic use. Several crystal structures have been published for NKA-CTS complexes, but they fail to explain the largely different inhibitory properties of the various CTSs. For instance, although CTSs are thought to inhibit ATPase activity by binding to NKA in the E2P state, we do not know if large conformational changes accompany binding, as no crystal structure is available for the E2P state free of CTS. Here, we describe crystal structures of the BeF3- complex of NKA representing the E2P ground state and then eight crystal structures of seven CTSs, including rostafuroxin and istaroxime, two new members under clinical trials, in complex with NKA in the E2P state. The conformations of NKA are virtually identical in all complexes with and without CTSs, showing that CTSs bind to a preformed cavity in NKA. By comparing the inhibitory potency of the CTSs measured under four different conditions, we elucidate how different structural features of the CTSs result in different inhibitory properties. The crystal structures also explain K+-antagonism and suggest a route to isoform specific CTSs.

Novel C3-Methylene-Bridged Indole Derivatives with and without Substituents at N1: The Influence of Substituents on Their Hemolytic, Cytoprotective, and Antimicrobial Activity.

Alkaloids are natural compounds useful as scaffolds for discovering new bioactive molecules. This study utilized alkaloid gramine to synthesize two groups of C3-substituted indole derivatives, which were either functionalized at N1 or not. The compounds were characterized by spectroscopic methods. The protective effects of the new compounds against in vitro oxidative hemolysis induced by standard oxidant 2,2'-azobis(2-amidinopropane dihydro chloride (AAPH) on human erythrocytes as a cell model were investigated. Additionally, the compounds were screened for antimicrobial activity. The results indicated that most of the indole derivatives devoid of the N1 substitution exhibited strong cytoprotective properties. The docking studies supported the affinities of selected indole-based ligands as potential antioxidants. Furthermore, the derivatives obtained exhibited potent fungicidal properties. The structures of the eight derivatives possessing indole moiety bridged to the imidazole-, benzimidazole-, thiazole-, benzothiazole-, and 5-methylbenzothiazoline-2-thiones were determined by X-ray diffraction. The C=S bond lengths in the thioamide fragment pointed to the involvement of zwitterionic structures of varying contribution. The predominance of zwitterionic mesomers may explain the lack of cytoprotective properties, while steric effects, which limit multiple the hydrogen-bond acceptor properties of a thione sulfur, seem to be responsible for the high hemolytic activity.

Solid State and Solution Structures of Lanthanide Nitrate Complexes of Tris-(1-napthylphosphine oxide).

Coordination complexes of lanthanide metals with tris-1-naphthylphosphine oxide (Nap3PO, L) have not been previously reported in the literature. We describe here the formation of lanthanide(III) nitrate complexes Ln(NO3)3L4 (Ln = Eu to Lu) and the structures of [Ln(NO3)3L2]·2L (Ln = Eu, Dy, Ho, Er) and L. The core structure of the complexes is an eight-coordinate [Ln(NO3)3L2] with the third and fourth ligands H-bonded via their oxygen atoms to one of the naphthyl rings. The structures are compared with those of the analogous complexes of triphenylphosphine oxide and show that the Ln-O(P) bond in the Nap3PO complexes is slightly longer than expected on the basis of differences in coordination numbers. The reaction solutions, investigated by 31P and 13C NMR spectroscopy in CD3CN, show that coordination of L occurs across the lanthanide series, even though complexes can only be isolated from Eu onwards. Analysis of the 31P NMR paramagnetic shifts shows that there is a break in the solution structures with a difference between the lighter lanthanides (La-Eu) and heavier metals (Tb-Lu) which implies a minor difference in structures. The isolated complexes are very poorly soluble, but in CDCl3, NMR measurements show dissociation into [Ln(NO3)3L2] and 2L occurs.

Synthesis, Structural Characterisation, and Electrochemical Properties of Copper(II) Complexes with Functionalized Thiosemicarbazones Derived from 5-Acetylbarbituric Acid.

The reaction between 5-acetylbarbituric acid and 4-dimethylthiosemicarbazide or 4-hexamethyleneiminyl thiosemicarbazide produces 5-acetylbarbituric-4-dimethylthiosemicarbazone (H2AcbDM) and 5-acetylbarbituric-4N-hexamethyleneiminyl thiosemicarbazone (H2Acbhexim). Eight new complexes with different copper(II) salts have been prepared and characterized using elemental analysis, molar conductance, UV-Vis, ESI-HRMS, FT-IR, magnetic moment, EPR, and cyclic voltammetry. In addition, three-dimensional molecular structures of [Cu(HAcbDM)(H2O)2](NO3)·H2O (3a), [Cu(HAcbDM)(H2O)2]ClO4 (4), and [Cu(HAcbHexim)Cl] (6) were determined by single crystal X-ray crystallography, and an analysis of their supramolecular structure was carried out. The H-bonded assemblies were further studied energetically using DFT calculations and MEP surface and QTAIM analyses. In these complexes, the thiosemicarbazone coordinates to the metal ion in an ONS-tridentate manner, in the O-enolate/S-thione form. The electrochemical behavior of the thiosemicarbazones and their copper(II) complexes has been investigated at room temperature using the cyclic voltammetry technique in DMFA. The Cu(II)/Cu(I) redox system was found to be consistent with the quasi-reversible diffusion-controlled process.

On Water Arrangements in Right- and Left-Handed DNA Structures.

DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.

Old Acquaintances and Novel Complex Structures for the Ni(II) and Cu(II) Complexes of bis-Chelate Oxime-Amide Ligands.

In the process of systematically studying the methylhydroxyiminoethaneamide bis-chelate ligands with polymethylene spacers of different lengths, L1-L3, and their transition metal complexes, a number of new Ni(II) and Cu(II) species have been isolated, and their molecular and crystal structures were determined using single-crystal X-ray diffraction. In all of these compounds, the divalent metal is coordinated by the ligand donor atoms in a square-planar arrangement. In addition, a serendipitously discovered new type of neutral Ni(II) complex, where the propane spacer of ligand L2 underwent oxidation to the propene spacer, and one of the amide groups was oxidised to the ketoimine, is also reported. The resulting ligand L2' affords the formation of neutral planar Ni(II) complexes, which are assembled in the solid state on top of each other, and yield two polymorphic structures. In both structures, the resulting infinite, exclusively parallel metal ion columns in ligand insulation may serve as precursor materials for sub-nano-conducting connectors. Overall, this paper reports the synthesis and characterisation of seven new anionic, cationic, and neutral Ni(II) and Cu(II) complexes, their crystal structures, as well as experimental and computed UV-Vis absorption spectra for two structurally similar Ni(II) complexes, yellow and red.

Unlocking the secrets of doxepin hydrochloride's crystal structure: Insights from high-quality powder diffraction analysis.

Doxepin hydrochloride, a versatile pharmaceutical compound, has been the subject of extensive research aimed at elucidating its crystal structure and solid-state characteristics. In this manuscript, we explore the significance of high-quality powder diffraction data in unveiling the intricate details of doxepin hydrochloride's crystal lattice. By examining the refined atom coordinates, density functional theory (DFT) optimization, and intermolecular interactions, we gain valuable insights into its structural conformation. This knowledge highlights the importance of precise crystallographic data in advancing our understanding of complex compounds and their pharmaceutical applications.

Cubic Iodide Lix YI3+x Superionic Conductors through Defect Manipulation for All-Solid-State Li Batteries.

Halide solid electrolytes (SEs) have attracted significant attention due to their competitive ionic conductivity and good electrochemical stability. Among typical halide SEs (chlorides, bromides, and iodides), substantial efforts have been dedicated to chlorides or bromides, with iodide SEs receiving less attention. Nevertheless, compared with chlorides or bromides, iodides have both a softer Li sublattice and lower reduction limit, which enable iodides to possess potentially high ionic conductivity and intrinsic anti-reduction stability, respectively. Herein, we report a new series of iodide SEs: Lix YI3+x (x=2, 3, 4, or 9). Through synchrotron X-ray/neutron diffraction characterizations and theoretical calculations, we revealed that the Lix YI3+x SEs belong to the high-symmetry cubic structure, and can accommodate abundant vacancies. By manipulating the defects in the iodide structure, balanced Li-ion concentration and generated vacancies enables an optimized ionic conductivity of 1.04 × 10-3  S cm-1 at 25 °C for Li4 YI7 . Additionally, the promising Li-metal compatibility of Li4 YI7 is demonstrated via electrochemical characterizations (particularly all-solid-state Li-S batteries) combined with interface molecular dynamics simulations. Our study on iodide SEs provides deep insights into the relation between high-symmetry halide structures and ionic conduction, which can inspire future efforts to revitalize halide SEs.

Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG.

Transcription of specific genes in bacteria under environmental stress is frequently initiated by extracytoplasmic function (ECF) σ factors. ECFs σ factors harbour two conserved domains, σ2 and σ4, for transcription initiation by recognition of the promoter region and recruitment of RNA polymerase (RNAP). The crystal structure of Streptomyces tsukubaensis SigG1, an ECF56-family σ factor, was determined revealing σ2, σ4 and the additional carboxi-terminal domain SnoaL_2 tightly packed in a compact conformation. The structure of anti-sigma RsfG was also determined by X-ray crystallography and shows a rare ß-barrel fold. Analysis of the metal binding motifs inside the protein barrel are consistent with Fe(III) binding, which is in agreement with previous findings that the Streptomyces tsukubaensis ECF56 SigG1-RsfG system is involved in metal-ion homeostasis.