The Homology Modeling and Docking Investigation of Human Cathepsin B

Background: Cathepsin B comprises a group of lysosomal cysteine proteases belonging to the Papain family; it has an intracellular function in the process of protein catabolism, antigen processing in the immune response, and Alzheimer’s disease. In cancers, cathepsin B interferes with autophagy and intracellular catabolism, and breaks down extracellular matrix, decreases protease inhibitors expression, and ultimately helps to accelerate metastasis, tumor malignancy, and reduce immune resistance. Methods: In this study, the 3D structure of cathepsin B was constructed using modeler and Iterative Threading ASSEmbly Refinement (I-TASSER), based on similarity to the crystallographic model of procathepsin B (1PBH). Then, the predicted cathepsin B model was evaluated using PROCHECK and PROSA for quality and reliability. Molecular studies suggested that the amino acids cysteine 108, histidine 189, and histidine 190 form the envelope of the active site of cathepsin B. The docking studies of cathepsin B was performed with protease inhibitors cystatin C, E-64 and leupeptin. Results: The lowest binding energy was related to the cathepsin B-E-64 complex. Accordingly, it was found that E64 interacts with the amino acid cysteine 108 of the active site of cathepsin B. Leupeptin made 2 hydrogen bonds with cathepsin B, but none with the active site of cathepsin amino acids. Cystatin C established a hydrogen bond with the arginine 18 of cathepsin B and made electrostatic bonds with aspartate 148 of cathepsin B. Conclusion: Therefore, the bioinformatics and docking studies of cathepsin B with its inhibitors could be used as reliable identification, treatment, and alternative methods for selecting the inhibitors and controllers of cancer progression

Reinforcement benefits of nanomodified coir fiber in lime-treated marine clay

In this study, reinforcing effect of nanomodified coir fibers with ferric hydroxide, Fe(OH)3, and aluminum hydroxide, Al(OH)3, on shear strength of limed marine clay soil was investigated. Accordingly, triaxial compression strength (TCS) testing was carried out to determine the shear strength parameters of the reinforced soil. Also, wetting/drying cycle testing was conducted to assess the durability of samples. The results from the experimental investigation show that the lime and nanomodified fibers improved the shear strength and durability through the intended modification on natural coir fiber. Moreover, an increase in the effective stress internal friction angle and the cohesion intercept were observed. To confirm the morphology alteration in fibers, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) tests were performed. Nanomodification of fibers increased their tensile strength and caused a better interaction with the limed matrix by an enhanced interfacial adhesion. The tensile strength and friction at the interface was the dominant mechanism controlling the reinforcement benefit

Effects of coir fibres modified with Ca(OH)2 and Mg(OH)2 nanopeprintss on mechanical properties of lime-treated marine clay

In this study, coir fibres were modified with nanoparticles of calcium hydroxide and magnesium hydroxide via a chemical treatment in order to increase the tensile strength of the fibres and their interaction with soil. To evaluate the modification and its effects, unconfined compressive strength tests, indirect tensile strength tests, flexural strength tests and triaxial compressive strength tests were carried out at 7, 28 and 90 days of curing age on lime-treated soil reinforced with modified and unmodified fibres. The obtained results showed that nano-modification of fibres enhanced the mechanical properties of the lime-treated clay soil due to the tensile strength of the augmented fibres. The results showed that the compressive strength, the indirect tensile strength and the flexural strength of samples treated with modified coir fibres increased by 64%, 122% and 56%, respectively compared to that of samples treated with unmodified fibres. Moreover, an increase in the effective internal friction angle and the cohesion intercept was observed. Also, the results of scanning electron microscopy and energy dispersive X-ray confirmed a desired alteration in morphology of the fibres

Enzymatic synthesis of phenyl fatty hydroxamic acids from canola and palm oils

Phenyl fatty hydroxamic acids (PFHAs) were synthesized from canola or palm oils and phenyl hydroxylamine (FHA) catalyzed by Lipozyme TL IM or RM IM. The reaction was carried out by shaking the reaction mixture at 120 rpm. The optimization was carried out by changing the reaction parameters, namely; temperature, organic solvent, amount and kind of enzyme, period of reaction and the mol ratio of reactants. The highest conversion was obtained when the reaction was carried out under the following conditions: temperature, 39°C; solvent, petroleum ether; kind and amount of lipase, 80 mg Lipozyme TL IM/mmol oil; reaction period, 72 h and FHA-oil ratio, 7.3 mmol FHA/ mmol oil. The highest conversion percentage of phenyl hydroxylaminolysis of the Ladan and Kristal brands commercial canola oils, palm stearin and palm kernel oils were 55.6, 52.2, 51.4 and 49.7 %, respectively

Preparation of fatty hydroxamic acid from canola oil.

Fatty hydroxamic acids were synthesized from canola oil by hydroxylaminolysis using lipozyme as catalyst. The products ware converted to copper fatty hydroxamate and precipitated in acetone. The precipitate was treated with nitric acid solution to release fatty hydroxamic acids and extracted to chloroform. The fatty hydroxamic acids were obtained by solvent evaporation under reduced pressure. Qualitative identification of hydroxamic acids were carried out by observing colour of the complexes with vanadium(V), iron(III) and copper(II) which were purple, dark red and green, respectively. The FTIR spectrum of the product showed the existence of the characteristic amide peaks at 3270 and 1642 cm -. Among four oil samples studied, canola oil of Ladan brand gave the highest yield of fatty hydroxamic acids

Jatropha curcas seed oil as new substrate for enzymatic methylhydroxylaminolysis.

Synthesis of methyl fatty hydroxamic acids (MFHAs) was carried out using lipozyme RM IM based on Jatropha Curcas seed oil. Optimized conditions were obtained at a mole ratio of 6/1 of methyl hydroxylamine/oil, temperature at 41˚C, enzyme 30mg/mmol and 72 h of reaction time. At this optimal condition, the yield% of methyl fatty hydroxamic based on Jatropha Curcas seed oil was 93.92%. The product was characterized by Fourier transform infrared (FTIR), and proton and carbon nuclear magnetic resonance (¹H-NMR and ¹³C NMR) spectra

Enzymatic synthesis of fatty hydroxamic acid derivatives based on palm kernel oil.

Fatty hydroxamic acid derivatives were synthesized using Lipozyme TL IM catalyst at biphasic medium as the palm kernel oil was dissolved in hexane and hydroxylamine derivatives were dissolved in water: (1) N-methyl fatty hydroxamic acids (MFHAs); (2) N-isopropyl fatty hydroxamic acids (IPFHAs) and (3) N-benzyl fatty hydroxamic acids (BFHAs) were synthesized by reaction of palm kernel oil and N-methyl hydroxylamine (N-MHA), N-isopropyl hydroxylamine (N-IPHA) and N-benzyl hydroxylamine (N-BHA), respectively. Finally, after separation the products were characterized by color testing, elemental analysis, FT-IR and 1H-NMR spectroscopy. For achieving the highest conversion percentage of product the optimum molar ratio of reactants was obtained by changing the ratio of reactants while other reaction parameters were kept constant. For synthesis of MFHAs the optimum mol ratio of N-MHA/palm kernel oil = 6/1 and the highest conversion was 77.8%, for synthesis of IPFHAs the optimum mol ratio of N-IPHA/palm kernel oil = 7/1 and the highest conversion was 65.4% and for synthesis of BFHAs the optimum mol ratio of N-BHA/palm kernel oil = 7/1 and the highest conversion was 61.7%

Artificial neural network modelling of photodegradation in suspension of manganese doped zinc oxide nanoparticles under visible-light irradiation

The artificial neural network (ANN) modeling of m-cresol photodegradation was carried out for determination of the optimum and importance values of the effective variables to achieve the maximum efficiency. The photodegradation was carried out in the suspension of synthesized manganese doped ZnO nanoparticles under visible-light irradiation. The input considered effective variables of the photodegradation were irradiation time, pH, photocatalyst amount, and concentration of m-cresol while the efficiency was the only response as output. The performed experiments were designed into three data sets such as training, testing, and validation that were randomly splitted by the software’s option. To obtain the optimum topologies, ANN was trained by quick propagation (QP), Incremental Back Propagation (IBP), Batch Back Propagation (BBP), and Levenberg-Marquardt (LM) algorithms for testing data set. The topologies were determined by the indicator of minimized root mean squared error (RMSE) for each algorithm. According to the indicator, the QP-4-8-1, IBP-4-15-1, BBP-4-6-1, and LM-4-10-1 were selected as the optimized topologies. Among the topologies, QP-4-8-1 has presented the minimum RMSE and absolute average deviation as well as maximum R-squared. Therefore, QP-4-8-1 was selected as final model for validation test and navigation of the process. The model was used for determination of the optimum values of the effective variables by a few three-dimensional plots. The optimum points of the variables were confirmed by further validated experiments. Moreover, the model predicted the relative importance of the variables which showed none of them was neglectable in this work

Application of methyl fatty hydroxamic acids based on Jatropha curcas seed oil and their metal complexes as anti microbial agents

Hydroxamic acids, fatty hydroxamic acids and their metal complexes are known as compounds that have biological activity. They have been investigated as antimicrobial compounds and were applied as antibacterial and antifungal agents in pharmacy andpharmaceutical compounds. In this research, the methyl fatty hydroxamic acids (MFHAs) based on Jatrophacurcas seed oil and their metal complexes include the copper (II) methyl fatty hydroxamate (Cu-MFHs) and iron (III) methyl fatty hydroxamate (Fe-MFHs) were prepared and applied as anti microbial agents against the Escherichia coli (E. coli), Proteus vulgaris (P. vulgaris) andProteus mirabilis (P. mirabilis) as gramnegative bacteria; methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (S. epidermidis) as gram-positive bacteria ; Candida parapsilosis (C. parapsilosis) and Candida Albicans(C. Albicans) as yeast family of fungi. The results showed that the antimicrobial activity of MFHAs, Cu-MFHs and Fe-MFHs increase while their amounts increase. Also metal complexation of MFHAs caused the anti microbial activity arise and this activity is higher for complexation by Cu(II) compared to that of Fe(III). Comparing antimicrobial activity of MFHAs, Cu-MFHs andFe-MFHs based on Jatrophacurcas seed oil with several antibiotic drugs such as ampicillin, chloramphenicol, gentamicin streptomycin, tetracycline and nystatin against the mentioned microbial showed that the Cu-MFHs andFe-MFHs have very strong antimicrobial activity

Well diffusion method for evaluation of antibacterial activity of copper phenyl fatty hydroxamate synthesized from canola and palm kernel oils.

Hydroxamic acids and their derivatives have low toxicities and show wide range of biological activities. Copper complexes of phenyl fatty hydroxamic acids (Cu-PFHs) were prepared in a biphasic organic / aqueous medium from phenyl fatty hydroxamic acids (PFHAs) and copper nitrate. The products were separated by decantation of organic phase from aqueous phase followed by evaporation of the solvent. Elemental analysis, UV-Vis spectra and FTIR spectra showed that Cu-PFHs were formed in the solution from the complexation of PFHAs and copper ion. The antibacterial activity of PFHAs and Cu-PFHs from canola and palm kernel oils were investigated against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) using well diffusion method. The results showed that Cu-PFHs have higher antibacterial activity compared to PFHAs. Antibacterial activity of Cu-PHAs from canola oil against E.coli was significantly higher than hloramphenicol and cefotaxime