Crystal Structure of Human CD47 in Complex with Engineered SIRPα.D1(N80A)

Background: Targeting the CD47/SIRPα signaling pathway represents a novel approach to enhance anti-tumor immunity. However, the crystal structure of the CD47/SIRPα has not been fully studied. This study aims to analyze the structure interface of the complex of CD47 and IMM01, a novel recombinant SIRPα-Fc fusion protein. Methods: IMM01-Fab/CD47 complex was crystalized, and diffraction images were collected. The complex structure was determined by molecular replacement using the program PHASER with the CD47-SIRPαv2 structure (PDB code 2JJT) as a search model. The model was manually built using the COOT program and refined using TLS parameters in REFMAC from the CCP4 program suite. Results: Crystallization and structure determination analysis of the interface of IMM01/CD47 structure demonstrated CD47 surface buried by IMM01. Comparison with the literature structure (PDB ID 2JJT) showed that the interactions of IMM01/CD47 structure are the same. All the hydrogen bonds that appear in the literature structure are also present in the IMM01/CD47 structure. These common hydrogen bonds are stable under different crystal packing styles, suggesting that these hydrogen bonds are important for protein binding. In the structure of human CD47 in complex with human SIRPα, except SER66, the amino acids that form hydrogen bonds are all conserved. Furthermore, comparing with the structure of PDB ID 2JJT, the salt bridge interaction from IMM01/CD47 structure are very similar, except the salt bridge bond between LYS53 in IMM01 and GLU106 in CD47, which only occurs between the B and D chains. However, as the side chain conformation of LYS53 in chain A is slightly different, the salt bridge bond is absent between the A and C chains. At this site between chain A and chain C, there are a salt bridge bond between LYS53 (A) and GLU104 (C) and a salt bridge bond between HIS56 (A) and GLU106 (C) instead. According to the sequence alignment results of SIRPα, SIRPβ and SIRPγ in the literature of PDB ID 2JJT, except ASP100, the amino acids that form common salt bridge bonds are all conserved. Conclusion: Our data demonstrated crystal structure of the IMM01/CD47 complex and provides a structural basis for the structural binding interface and future clinical applications.     

3dDNA: A Computational Method of Building DNA 3D Structures

Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains.     

Identification of Protosappanoside D from Caesalpinia decapetala and Evaluation of Its Pharmacokinetic,Metabolism and Pharmacological Activity

Protosappanoside D (PTD) is a new component isolated from the extract of Caesalpinia decapetala for the first time. Its structure was identified as protosappanin B-3-O-β-D-glucoside by ¹H-NMR, ¹³C-NMR, 2D-NMR and MS techniques. To date, the pharmacological activities, metabolism or pharmacokinetics of PTD has not been reported. Therefore, this research to study the anti-inflammatory activity of PTD was investigated via the LPS-induced RAW264.7 cells model. At the same time, we also used the UHPLC/Q Exactive Plus MS and UPLC-MS/MS methods to study the metabolites and pharmacokinetics of PTD, to calculate its bioavailability for the first time. The results showed that PTD could downregulate secretion of the pro-inflammatory cytokines. In the metabolic study, four metabolites were identified, and the primary degradative pathways in vivo involved the desaturation, oxidation, methylation, alkylation, dehydration, degradation and desugarization. In the pharmacokinetic study, PTD and its main metabolite protosappanin B (PTB) were measured after oral and intravenous administration. After oral administration of PTD, its T_max was 0.49 h, t_1/2z and MRT_(0–t) were 3.47 ± 0.78 h and 3.06 ± 0.63 h, respectively. It shows that PTD was quickly absorbed into plasma and it may be eliminated quickly in the body, and its bioavailability is about 0.65%.     

Sodium β-Diketonate Glyme Adducts as Precursors for Fluoride Phases: Synthesis,Characterization and Functional Validation

Very few sodium complexes are available as precursors for the syntheses of sodium-based nanostructured materials. Herein, the diglyme, triglyme, and tetraglyme (CH₃O(CH₂CH₂O)_nCH₃, n = 2–4) adducts of sodium hexafluoroacetylacetonate were synthesized in a single-step reaction and characterized by IR spectroscopy, ¹H, and ¹³C NMR. Single-crystal X-ray diffraction studies provide evidence of the formation of the ionic oligomeric structure [Na₄(hfa)₆]²⁻•2[Na(diglyme₂]⁺ when the diglyme is coordinated, while a mononuclear seven-coordinated complex Na(hfa)•tetraglyme is formed with the tetraglyme. Reaction with the monoglyme (CH₃OCH₂CH₂OCH₃) does not occur, and the unadducted polymeric structure [Na(hfa)]_n forms, while the triglyme gives rise to a liquid adduct, Na(hfa)•triglyme•H₂O. Thermal analysis data reveal great potentialities for their applications as precursors in metalorganic chemical vapor deposition (MOCVD) and sol-gel processes. As a proof-of-concept, the Na(hfa)•tetraglyme adduct was successfully applied to both the low-pressure MOCVD and the sol-gel/spin-coating synthesis of NaF films.     

Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films

We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm^–1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm⁻¹ that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.     

Ionic Dioxidovanadium(V) Complexes with Schiff-Base Ligands as Potential Insulin-Mimetic Agents—Substituent Effect on Structure and Stability

Four dioxidovanadium(V) complexes with Schiff-base ligands based on 2-hydroxybenzhydrazide with four different substituted salicylaldehydes (5-chlorosalicylaldehyde, 3,5-dichlorosalicylaldehyde, 5-nitrosalicylaldehyde, 3-bromo-5-chlorosalicylaldehyde) were synthesized and described, by using V₂O₅ and triethylamine. The single crystal X-ray structure measurements as well as elemental analyses and IR spectra confirmed the formulas of the ionic complexes with a protonated triethylamine acting as counterion, HTEA[VO₂(L)] (HL = Schiff-base ligand). The kinetic stability of the complexes at pH = 2 and 7 was discussed with respect to the neutral vanadium(V) complexes previously studied as potential insulin-mimetic agents. A correlation between the substituents in an aromatic ring of the Schiff-base ligands with crystal packing, and also with the stability of the compounds, was presented.     

Thermal and Structural Characterization of Two Crystalline Polymorphs of Tafamidis Free Acid

Tafamidis, chemical formula C₁₄H₇Cl₂NO₃, is a drug used to delay disease progression in adults suffering from transthyretin amyloidosis, and is marketed worldwide under different tradenames as a free acid or in the form of its meglumine salt. The free acid (CAS no. 594839-88-0) is reported to crystallize as distinct (polymorphic) crystal forms, the thermal stability and structural features of which remained thus far undisclosed. In this paper, we present—by selectively isolating highly pure batches of Tafamidis Form 1 and Tafamidis Form 4—the full characterization of these solids, in terms of crystal structures (determined using state-of-the-art structural powder diffraction methods) and spectroscopic and thermal properties. Beyond conventional thermogravimetric and calorimetric analyses, variable-temperature X-ray diffraction was employed to measure the highly anisotropic response of these (poly)crystalline materials to thermal stimuli and enabled the determination of the linear and volumetric thermal expansion coefficients and of the related indicatrix. Both crystal phases are monoclinic and contain substantially flat and π-π stacked Tafamidis molecules, arranged as centrosymmetric dimers by strong O-H···O bonds; weaker C-H···N contacts give rise, in both polymorphs, to infinite ribbons, which guarantee the substantial stiffness of the crystals in the direction of their elongation. Complete knowledge of the structural models will foster the usage of full-pattern quantitative phase analyses of Tafamidis in drug and polymorphic mixtures, an important aspect in both the forensic and the industrial sectors.     

Structural Basis for (2R,3R)-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus

The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by a reverse Michael addition. The overall fold and the constitution of the active site of the enzyme completely differ from the well-characterised chalcone isomerase of plants. For (+)-taxifolin, CHI catalyses the intramolecular ring contraction to alphitonin. In this study, Fwe perform crystal structure analyses of CHI and its active site mutant His33Ala in the presence of the substrate taxifolin at 2.15 and 2.8 Å resolution, respectively. The inactive enzyme binds the substrate (+)-taxifolin as well defined, whereas the electron density maps of the native CHI show a superposition of substrate, product alphitonin, and most probably also the reaction intermediate taxifolin chalcone. Evidently, His33 mediates the stereospecific acid-base reaction by abstracting a proton from the flavonoid scaffold. The stereospecificity of the product is discussed.     

Variable Dimensionality of Europium(III) and Terbium(III) Coordination Compounds with a Flexible Hexacarboxylate Ligand

A reaction between 4,4′,4″-(benzene-1,3,5-triyltris(oxy))triphthalic acid (H₆L) and lanthanide(III) nitrates (Ln = Eu³⁺, Tb³⁺) in water under the same conditions gave a molecular coordination compound [Tb(H_4.5L)₂(H₂O)₅]∙6H₂O in the case of terbium(III) and a one-dimensional linear coordination polymer {[Eu₂(H₃L)₂(H₂O)₆]∙8H₂O}_n in the case of europium(III). The crystal structures of both compounds were established by single-crystal X-ray diffraction, and they were further characterized by powder X-ray diffraction, thermogravimetric analysis and infrared spectroscopy. The compounds demonstrated characteristic lanthanide-centered photoluminescence. The lanthanide-dependent dimensionality of the synthesized compounds, which are the first examples of the coordination compounds of hexacarboxylic acid H₆L demonstrates its potential as a linker for new coordination polymers.