Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification

Cyanide is a hazardous and detrimental chemical that causes the inactivation of the respiration system through the inactivation of cytochrome c oxidase. Because of the limitation in the number of cyanide-degrading enzymes, there is a great demand to design and introduce new enzymes with better functionality. This study developed an integrated method of protein-homology-modelling and ligand-docking protein-design approaches that reconstructs a better active site from cyanide hydratase (CHT) structure. Designing a mutant CHT (mCHT) can improve the CHT performance. A computational design procedure that focuses on mutation for constructing a new model of cyanide hydratase with better activity was used. In fact, this study predicted the three-dimensional (3D) structure of CHT for subsequent analysis. Inducing mutation on CHT of Trichoderma harzianum was performed and molecular docking was used to compare protein interaction with cyanide as a ligand in both CHT and mCHT. By combining multiple designed mutations, a significant improvement in docking for CHT was obtained. The results demonstrate computational capabilities for enhancing and accelerating enzyme activity. The result of sequence alignment and homology modeling show that catalytic triad (Cys-Glu-Lys) was conserved in CHT of Trichoderma harzianum. By inducing mutation in CHT structure, MolDock score enhanced from −18.1752 to −23.8575, thus the nucleophilic attack can occur rapidly by adding Cys in the catalytic cavity and the total charge of protein in pH 6.5 is increased from −6.0004 to −5.0004. Also, molecular dynamic simulation shows a stable protein-ligand complex model. These changes would help in the cyanide degradation process by mCHT.     

Flavones and rosmarinic acid from Salvia limbata

The genus Salvia (Lamiaceae) contains more than 50 shrub species in Iran, and Salvia limbata C.A. Meyer grows widely in the north and central parts of the country. Six flavones and rosmarinic acid were isolated from the ethyl acetate and methanol extracts of the flowered aerial parts of S. limbata collected from Semnan province. The separation process was carried out using several chromatographic methods. Structural elucidation was based on NMR data, in comparison with those reported in the literature. The isolated compounds were identified as ladanein (1), salvigenin (2), luteolin 7-methyl ether (3), cirsiliol (4), eupatorin (5), luteolin 7-O-glucoside (6) and rosmarinic acid (7). Some of these flavonoids have been reported to show antibacterial and cytotoxic activities.     

Bio‐assisted synthesized Ag(0) nanoparticles immobilized on SBA‐15/cyclodextrin nanosponge adduct: Efficient heterogeneous catalyst for the ultrasonic‐assisted synthesis of benzopyranopyrimidines

For the first time, SBA‐15/cyclodextrin nanosponge adduct was synthesized through reaction of Cl‐functionalized SBA‐15 and amine‐functionalized cyclodextrin nanosponge (CDNS). This adduct, which benefits from features of both SBA‐15 and CDNS, was then used for immobilization of Ag(0) nanoparticles which were prepared and capped using a bio‐based approach. Ag@CDNS–SBA‐15 was applied as a heterogeneous catalyst for promoting the three‐component reaction of benzaldehydes, 4‐hydroxycoumarin and urea or thiourea under ultrasonic irradiation to furnish benzopyranopyrimidines. The reaction variables were optimized using response surface methodology. The catalytic activity of Ag@CDNS–SBA‐15 was higher than those of Ag@CDNS, Ag@SBA‐15 and Ag@SBA‐15 + CDNS, confirming the contribution of both components to catalysis as well as a synergistic effect between CDNS and SBA‐15. The role of CDNS was to accommodate the substrates and bring them to the vicinity of the Ag(0) nanoparticles. Notably the catalyst was reusable and could be recovered and reused for up to four reaction runs with slight Ag(0) leaching and loss of catalytic activity.     

HPA decorated Halloysite Nanoclay: An efficient catalyst for the green synthesis of Spirooxindole derivatives

A novel heterogeneous catalyst, HPA@HNTs‐IMI‐SO₃H, was designed and synthesized based on functionalization of halloysite nanotubes with ionic liquid and subsequent incorporation of heteropolyacid. The structure of the catalyst was studied and confirmed by using SEM/EDX, FTIR, XRD, ICP‐AES, TGA, DTGA and BET. Moreover, the catalytic activity of HPA@HNTs‐IMI‐SO₃H was investigated for promoting ultrasonic‐assisted three‐component reaction of isatines, malononitrile or cyanoacetic esters and 1,3‐dicarbonyl compounds to afford corresponding spirooxindole in high yields and short reaction time. The reusability of the catalyst was also studied. Notably, the catalyst could be recovered and reused for three reaction runs. However, reusing for fourth reaction runs led to the decrease of the catalytic activity. Considering leaching test results, that observation was attributed to the leaching of heteropolyacids, which can be induced by ultrasonic irradiation.     

Green bio‐based synthesis of Fe2O3@SiO2‐IL/Ag hollow spheres and their catalytic utility for ultrasonic‐assisted synthesis of propargylamines and benzo[b]furans

A novel magnetic hybrid system containing nano‐magnetic Fe₂O₃ hollow spheres, silica shell, [pmim]Cl ionic liquid and silver nanoparticles was synthesized and characterized. The silver nanoparticles were prepared via biosynthesis using Achillea millefolium flower as reducing and stabilizing agent. The hybrid system was successfully used as an efficient and reusable catalyst for promoting green ultrasonic‐assisted A³ and KA² coupling reactions as well as benzo[b]furan synthesis. It was found that decoration of the magnetic core with non‐magnetic moieties decreased the maximum saturation magnetization. However, the catalyst was still superparamagnetic and could be simply separated from the reaction mixture using an external magnet. The heterogeneous nature of the catalyst was also confirmed by studying its reusability and stability and the leaching of silver. Use of aqueous media, high yields, short reaction times, broad substrate tolerance and low required amount of catalyst are the merits of this protocol.