N-glycosylation of High Mobility Group Box 1 protein (HMGB1) modulates the interaction with glycyrrhizin: A molecular modeling study

High Mobility Group Box 1 protein (HMGB1) is an abundant protein with multiple functions in cells, acting as a DNA chaperone and damage-associated molecular pattern molecule. It represents an attractive target for the treatment of inflammatory diseases and cancers. The plant natural product glycyrrhizin (GLR) is a well-characterized ligand of HMGB1 and a drug used to treat diverse liver and skin diseases. The drug is known to bind to each of the two adjacent HMG boxes of the non-glycosylated protein. In cells, HMGB1 is N-glycosylated at three asparagine residues located in boxes A and B, and these N-glycans are essential for the nucleocytoplasmic transport of the protein. But the impact of the N-glycans on drug binding is unknown. Here we have investigated the effect of the N-glycosylation of HMGB1 on its interaction with GLR using molecular modelling, after incorporation of three N-glycans on a Human HMGB1 structure (PDB code 2YRQ). Sialylated bi-antennary N-glycans were introduced on the protein and exposed in a folded or an extended conformation for the drug binding study. The docking of the drug was performed using both 18α- and 18β-epimers of GLR and the conformations and potential energy of interaction (ΔE) of the different drug-protein complexes were compared. The N-glycans do not shield the drug binding sites on boxes A and B but can modulate the drug-protein interaction, via both direct and indirect effects. The calculations indicate that binding of 18α/β-GLR to the HMG box is generally reduced when the protein is N-glycosylated vs. the non-glycosylated protein. In particular, the N-glycans in an extended configuration significantly weaken the binding of GLR to box-B. The effects of the N-glycans are mostly indirect, but in one case a direct contact with the drug, via a carbohydrate-carbohydrate interaction, was observed with 18β-GLR bound to Box-B of glycosylated HMGB1. For the first time, it is shown (at least in silico) that N-glycosylation, one of the many post-translational modifications of HMGB1, can affect drug binding.     

N-glycosylation and ubiquitinylation of PD-L1 do not restrict interaction with BMS-202: A molecular modeling study

The Programmed cell Death protein-1/Ligand 1 (PD-1/L1) checkpoint is a major target in oncology. Monoclonal antibodies targeting PD-1 or PD-L1 are used to treat different types of solid tumors and lymphoma. PD-L1-binding small molecules are also actively searched. The lead compound is the biphenyl drug BMS-202 which stabilizes PD-L1 protein dimers and displays a potent antitumor activity in experimental models. Here we have investigated the effect of N-glycosylation (at N35, N192, N200 and N219) and mono-ubiquitination (at K178) of PD-L1 on the interaction with BMS-202 by molecular modeling. Two complementary tridimensional models of PD-L1, based on available crystallographic structures, were constructed with BMS-202 bound. The structures were glycosylated, with a fucosylated bi-antennary N-glycan and ubiquitinated. Model 1 refers to glycoPD-L1 bearing 16 N-glycans, with or without 4 ubiquitin residues. Model 2 presents 8 N-glycans and 2 ubiquitin residues. In both cases, BMS-202 was bound to the protein interface, stabilizing a PD-L1 dimer. The incorporation of the N-glycans or the ubiquitins did not significantly alter the drug-protein recognition. The interface of the drug-stabilized protein dimer is unaffected by the glycosylation or ubiquitination. Calculations of the binding energies indicated that the glycosylation slightly reduces the stability of the drug-protein complexes but does not prevent the drug binding process. Our modeling study suggests that the drug can target efficiently the different forms of PD-L1 in cells, glycosylated, ubiquitinated or not. These models of N-glycosylated and ubiquitinated PD-L1 will be useful to study other PD-L1 protein complexes.     

Structure-activity analysis of fluorinated 1-N-arylamino-1-arylmethane-phosphonic acid esters as inhibitors of the NADH:ubiquinone oxidoreductase (complex I)

Summary The structural and electronic properties of fluorinated 1-N-arylamino-1-arylmethanephosphonic acid esters were studied and related to the inhibitory effects on NADH:ubiquinone oxidoreductase (complex I). Electrostatic potential surfaces, dipole moments and molecular geometries were analysed. Based on the conformational analysis and the electronic parameters, a simple model for the active site of the fluorinated 1-N-arylamino-1-arylmethanephosphonic acid esters was developed, explaining the inhibitory power. The strongest inhibition effects were found for the 1-(N-4-trifluoromethoxyphenyl)-amino-1-phenylmethanephosphonic acid diethyl ester 1bab.     

Synthesis,characterization, and DNA band of a five-coordinate cadmium(II) complex with 1,3-bis(1-benzylbenzimidazol-2-yl)-2-thiapropane

A five-coordinate cadmium(II) complex with 1,3-bis(1-benzylbenzimidazol-2-yl)2-thiapropane (L), [Cd(L)Br₂]?·?DMF, has been synthesized and characterized by elemental analysis, electrical conductivities, IR, and UV-Vis spectral measurements. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. The Cd(II) is five-coordinate with two nitrogens and a sulfur from one ligand, and two bromides. The N₂SBr₂ donors are in a distorted square-pyramidal geometry (τ?=?0.32). Electronic absorption titration spectra, EB (ethidium bromide) competitive experiment, and viscosity measurement indicated that the complex can bind to DNA via intercalation.     

异咯嗪修饰富勒烯-聚丙烯酸的合成及其与DNA的相互作用

利用自由基聚合反应合成了聚丙烯酸修饰的富勒烯(C₆₀-PAA),进一步通过酯化反应将核黄素类似物6,7-二甲基-9-(2’-羟乙基)-异咯嗪(DHIX)与C₆₀-PAA共价连接,得到C₆₀-PAA-DHIX.利用傅立叶红外光谱(FT-IR)、核磁共振氢谱(¹HNMR)、紫外-可见吸收光谱(UV-Vis)、荧光光谱对产物的化学结构进行了表征.循环伏安法表明,C₆₀-PAA-DHIX中富勒烯基团的第一还原电位要高于DHIX基团的第一还原电位.ESR实验表明C₆₀-PAA-DHIX能与N,N-二甲基苯胺发生多步光诱导电子转移反应,即DHIX基团与N,N-二甲基苯胺发生光诱导电子转移生成DHIX负离子自由基(DHIX^-·),DHIX^-·能进一步将电子传递给富勒烯生成富勒烯负离子自由基.DNA熔解曲线、紫外-可见吸收光谱和荧光光谱结果表明,C₆₀-PAA-DHIX通过沟槽结合与CTDNA作用,而C₆₀-PAA与DNA的作用较弱.无氧条件下,C₆₀-PAA-DHIX具有比C₆₀-PAA更强的DNA光损伤能力.     

Ternary copper(II) complex of 1,10-phenanthroline and L-glycine: crystal structure and interaction with DNA

A ternary copper(II) complex, [Cu(phen)(L-Gly)(H₂O)] ·?NO₃ ·?1.5H₂O (phen =?1,10-phenanthroline, L-Gly =?L-glycine), has been synthesized and structurally characterized. The complex crystallized in a monoclinic system with space group C2/c, a =?20.572(3) Å, b =?6.9987(10) Å, c =?23.561(3) Å, β?= 98.776(5)°. The five-coordinate copper(II) center is a distorted square pyramid. Absorption spectra, fluorescence spectra and viscosity measurements showed interaction between the copper complex and DNA through an intercalative mode. The complex exhibited efficient DNA cleavage activity at micromolar concentration in the presence of ascorbate with hydroxyl radicals as the active species.     

Cytotoxic copper(II) complex of tripyridoquinoxaline with DNA hydrolase activity

A monomeric copper(II) complex, [Cu(tpq)₂(H₂O)₂](ClO₄)₂, (tpq = tripyridoquinoxaline), has been synthesized and characterized spectroscopically. This complex has been found to bind DNA intercalatively and the DNA binding constant, K_b, for this complex has been determined from absorption measurements and was found to be (5.7 ± 0.3) × 10³ M⁻¹. This complex successfully promotes hydrolytic cleavage of plasmid DNA, producing single and double DNA strand breaks in the absence of any added cofactor. The amount of conversion of the supercoiled form of plasmid to the nicked circular form depends on the concentration of the copper complex as well as the duration of the incubation of the complex with DNA. The rate of conversion of SC to NC has been determined to be 2.65 × 10⁻⁴ s⁻¹ at pH 7.2 in the presence of 80 μM of the complex. This complex has also been shown to be cytotoxic towards A549 lung adenocarcinoma cells. This complex has been shown to bring about apoptosis of the cancerous A549 cell line.     

A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2

The exact residues within severe acute respiratory syndrome coronavirus (SARS-CoV) S1 protein and its receptor, human ACE2, involved in their interaction still remain largely undetermined. Identification of exact amino acid residues that are crucial for the interaction of S1 with ACE2 could provide working hypotheses for experimental studies and might be helpful for the development of antiviral inhibitor. In this paper, a molecular docking model of SARS-CoV S1 protein in complex with human ACE2 was constructed. The interacting residue pairs within this complex model and their contact types were also identified. Our model, supported by significant biochemical evidence, suggested receptor-binding residues were concentrated in two segments of S1 protein. In contrast, the interfacial residues in ACE2, though close to each other in tertiary structure, were found to be widely scattered in the primary sequence. In particular, the S1 residue ARG453 and ACE2 residue LYS341 might be the key residues in the complex formation.     

联吡啶衍生物芳基钌配合物的合成及其与DNA、蛋白质相互作用

以2种配体4,4′-dimethyl-2,2′-bipyridine(L1)和4′-methyl-(2,2′-bipyridine)-4-carbaldehyde oxime(L2),分别与芳基钌二聚体[RuCl_2(η~6-p-cymene)]2合成了2种新型单核配合物[Ru(η~6-p-cymene)(L1)Cl]Cl(1)和[Ru(η6-p-cymene)(L2)Cl]Cl(2)。应用元素分析、ESI-MS和~1H NMR对配合物的组成和结构进行表征,通过紫外光谱法和荧光光谱法研究了配合物的水解及其与CT-DNA和血清蛋白的结合性质,并且进行了细胞毒性研究。结果表明,在水溶液中配合物1比2在动力学上更稳定(k:0.383 h~(-1)(1)、1.458 h~(-1)(2));配合物均通过嵌入作用与双链DNA结合,但2有较强的结合能力(Kb:7.8×10~3L·mol~(-1)(1)、1.86×10~4L·mol~(-1)(2))。配合物均能与蛋白质发生相互作用,引起蛋白静态猝灭,但1作用较强(KA:1.04×10~5L·mol~(-1)(1)、8.62×10~4L·mol~(-1)(2))。配合物与蛋白的较强结合能力,可能是其细胞毒性不高的原因。     

Structural,functional, and evolutionary analysis of late embryogenesis abundant proteins (LEA) in Triticum aestivum: A detailed molecular level biochemistry using in silico approach

LEA (Late Embryogenesis Abundant) proteins are abundant in plants and play a crucial role in abiotic stress tolerance. In our work, we primarily focused on the variations in physiochemical properties, conserved domains, secondary structure, gene ontology and evolutionary relationships among 40 LEA proteins of Triticum aestivum (common wheat). Wheat LEA protein belongs to first 6 classes out of the 13 classes present in LEApdB, the comprehensive database for LEA proteins. Proteins belonging to each LEApdB class have structures and functions distinguished from other classes. The study found three different conserved LEA domains in Triticum aestivum. One important domain was dehydrin, present in wheat proteins of classes 1, 2 and 4, though varied in sequence level, have similar biological processes. The study also found sequence level and phylogenetic similarity between dehydrin domains of class 1 and 4, but distinct from that of LEApdB class 2. This study also demonstrated functional diversity in two class 6 proteins occurred due to many destabilizing mutations in the LEA4 domain that caused alteration of ligand binding and conformational shift from 3₁₀-helix → turn within the domain. The LEA4 domains of these proteins also showed functional similarity and evolutionary relatedness with three other proteins of genus Aegilops, denoting that these proteins in Triticum aestivum were derived from its ancestor Aegilops. The study also assigned LEApdB class 4 to an unclassified LEA protein ‘WZY2-1’ based on amino acid composition, conserved domain, motif architecture and phylogenetic relatedness with class 4 proteins. Our study has revealed a detailed analysis of LEA proteins in Triticum aestivum and can serve as a pillar for further investigations and comparative analysis of wheat LEA proteins with other cereal or plant types.     

Is samoquasine A indeed benzo[f]phthalazin-4(3H)-one? Unambiguous, straightforward synthesis of benzo[f]phthalazin-4(3H)-one and its regioisomer benzo[f]phthalazin-1(2H)-one

In search for the structural elucidation of samoquasine A, a natural product isolated from the seeds of Annona squamosa L., two benzo[f]phthalazinone isomers have been synthesized. The synthetic pathway followed to build up these skeletons is based on the combination of two Suzuki reactions on a pyridazinone precursor and a ring closure reaction via a condensation reaction. ¹H NMR data of the synthesized compound allowed to establish that the structure of the natural product samoquasine A is not benzo[f]phthalazin-4(3H)-one, as previously suggested.     

Monomodal polyelectrolyte complex nanoparticles of PDADMAC/Poly(styrenesulfonate): preparation and protein interaction

The binding of the model proteins HSA, LYZ and MYO to PEC nanoparticles is reported. PEC particles were prepared by mixing solutions of PDADMAC either with PSS or PMA-MS, followed by consecutive centrifugation. Monomodal anionic (PEC-1.50) and cationic (PEC-0.66) PEC particles were obtained using non-stoichiometric mixing ratios. PEC/protein conjugates were prepared by adding charged protein solutions to dispersions of respective like charged PEC particles, followed by one centrifugation step. Mixing proteins and PEC particles under attractive conditions led to flocculation of the dispersion. From CD, DLS and AFM the following trend for protein binding at PEC particles under repulsive conditions was obtained: HSA/PEC-1.50 > MYO/PEC-1.50 > LYZ/PEC-0.66. Protein uptakes up to 0.33 g x g(-1) (protein/PEC) (CD) and particle diameter enlargements up to 13 nm (AFM) were obtained at c(PROT) = 0.091 mg . mL(-1). Furthermore, novel spin coated films of PEC particles were interacted with proteins under both repulsive and attractive conditions. In-situ ATR FT-IR spectroscopy revealed that the adsorbed amount of HSA and LYZ under attractive conditions was significantly higher than under repulsive ones, which is analogous to protein adsorption at polyelectrolyte multilayers terminated either by polycation or polyanion. Similarly to the dispersed PEC/protein conjugates, under repulsive conditions the uptake of HSA was higher compared to LYZ. The shown protein uptake under repulsive conditions is related to concepts of mild enzyme or protein binding at nonbiogenic substrates.     

Synthesis of a New Cobalt (II) Complex and its Interaction with DNA

The interaction of metal complexes with DNA has been widely studied by differentmethods such as spectrophotometry, light scattering technique, fluorometry1-3. Manycomplexes such as Co(phen)2 ,Co(en)2 ,Fe(EDTA)2- etc.4,5 have been synthesized and 3+ 3+their effect on DNA has been studied in order to further explain the mechanism of genemutation, anti-cancer or cancer-induced reason and DNA targeted drugs. In this paper,a new cobalt complex was synth…     

A Novel Molecule: 1-(2,6 Dichlorobenzyl)-4-(2-(2-4-hydroxybenzylidene)hydrazinyl)pyridinium Chloride and its Interaction with DNA

Herein, a novel pyridine derivative, 1-(2,6 dichlorobenzyl)-4-(2-(2-4-hydroxybenzylidene)hydrazinyl)-pyridinium chloride (DHPC), was synthesized as a candidate drug molecule. Interaction of DHPC with DNA was used to explore its effect on DNA via Differential Pulse Voltammetry, Cyclic Voltammetry, and Electrochemical Impedance Spectroscopy. We demonstrated that oxidation signal of guanine bases of DNA decreased significantly while that of DHPC increased after its interaction with one another. Our candidate drug molecule exhibits LOD and LOQ, e.g., 1.5 μg/mL and 4.9 μg/mL, respectively. Toxicity effect value for DHPC (S%) was calculated as %31, demonstrating the candidate drug molecule's toxic effect on DNA.     

13 C NMR Studies of the Interaction of Gold(I) Thiomalate with 6-Mercaptopurine and Its Derivatives

The interaction of gold(I) thiomalate, [Autm] n with thiolated nucleosides, 6-mercaptopurine (6-MP), 6-mercaptopurine-9- g - D -riboside (6-MPR) and 2-amino-6-mercaptopurine-9- g - D -riboside (2-A-6-MPR) has been studied by 1 H and 13 C NMR spectroscopy. It has been observed that these thiolated purine bases break the [Autm] n polymer and form complexes of the type $[\rangle \!{\rm C} {{\hskip -1.7pt \openup -13pt \eqalign{\displaystyle{-\!\!-}\cr\displaystyle{-\!\!-}}\hskip -1.7pt}}\hbox{{\rm S}-{\rm Au-tm}]}$     

Bis(1-methylbenzotriazole)dinitratocobalt(II): A pseudo-octahedral complex with pseudo-tetrahedral magnetochemical and ligand field characteristics

Summary The reaction between cobalt(II) nitrate and 1-methylbenzotriazole (MeBTA) leads to a complex with unusual magnetochemical and ligand field characteristics. The synthesis and the physical and spectroscopic properties of the pseudo-octahedral complex [Co(MeBTA)₂(NO₃)₂] are described.

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Bis(1-methylbenzotriazol)dinitratocobalt(II): Ein pseudo-octaedrischer Komplex mit pseudotetraedrischen magnetochemischen und Ligandenfeld-Charakteristika (Kurze Mitt.)

Zusammenfassung Die Reaktion zwischen Kobalt(II)nitrat und 1-Methylbenzotriazol (MeBTA) führt zu einem Komplex mit ungewöhnlichen magnetochemischen und Ligandenfeld-Eigenschaften. Die Synthese und die spektroskopischen Eigenschaften des pseudo-octaedrischen Komplexes [Co(MeBTA)₂(NO₃)₂] werden beschrieben.

     

Shellfish waste-derived mesoporous chitosan for impressive removal of arsenic(V) from aqueous solutions: A combined experimental and computational approach

Novel shellfish waste-derived chitosan (CS) has been developed to adsorb As(V) from simulated wastewater under evaluating adsorption process parameters. The coexistence of some competing ions, like SiO₃^2-, Cl^-, NO₃^– and PO₄^3- as well as the regeneration capacity of the spent adsorbent, was explored. The experimental data were modeled using several kinetics and isotherm models to understand the mechanism related to the uptake process. As(V) uptake was relatively rapid and highly dependent on pH. The Avrami-fractional-order expression supported data best, while the Liu equation described well isotherm data at pH 5.0. The maximum uptake capability (Liu) was 12.32 mg/g, and the highest removal performance (99 %) was obtained at optimum pH 5.0. Molecular dynamics simulations were performed to more clearly illuminate the atomic-level interactions between arsenic species and CS surface in both acidic and basic mediums. After four adsorption–desorption cycles, CS exhibited more than 90 % As(V) removal efficiency. The results of this study indicates that low cost shellfish derived chitosan is promising for efficient removal of As(V) from water body and can be used to remove other pollutants from watewater.     

Characterization of the malate-aluminum(III) complex using 1H and 27Al NMR spectroscopy

Structural elucidation of a malate-aluminum(III) complex has been carried out using 1H and 27Al NMR spectroscopy. The 1H chemical shift perturbation clearly indicated the interaction between malate and Al(III) ion. The measurements of 27Al NMR and 1H-13C HSQC spectra demonstrated that the major form of a complex comprised two equivalent malate ions and two unequivalent Al(III) ions. With this constraint, an equilibrium geometry of the complex was proposed by a semi-empirical molecular orbital calculation.