《Computational Biology and Chemistry》2019

Novel azo linked substituted benzimidazole, benzoxazole, and benzothiazole were synthesized by diazo coupling and characterized by ¹H NMR, elemental analysis, FTIR and UV–vis spectroscopy. The newly synthesized compounds were evaluated for invitro antibacterial activity against Staphylococcus aureus and Escherichia Coli strains by Resazurin microtiter assay method (REMA). The minimum inhibitory concentration (MIC in μg/mL) were used to express the antibacterial activities. The azo linked compounds exhibited good to moderate or high antibacterial activities in vitro. Computational studies were performed to correlate HOMO-LUMO gap with antibacterial activity. The comparative molecular docking studies revealed better insights into binding mechanisms.  相似文献   

    

《Computational Biology and Chemistry》2019

In this paper, we have established methylenebis (4-hydroxy-2H-chromen-2-one) as a promising anticancer scaffold with kinesin spindle protein (KSP) inhibitory activity under malignant condition. A series of biscoumarin derivatives (MN1 to MN30) with different substituent were synthesized, and their anticancer activity was explored. Six biscoumarin derivatives that were found active were further selected to formulate organic nanoparticles (ONPs). Anticancer activity of both the forms (viz conventional and ONPs) was compared. MN30 was found most potent whereby MN10 showed good anticancer activity in both, i.e., conventional and ONP form; the structural activity relationship (SAR) study has been established. Computational investigation revealed biscoumarin scaffold as a suitable pharmacophore to bind against KSP protein. Molecular dynamics simulation studies revealed protein-ligand stability and dynamic behavior of biscoumarin-KSP complex. Finally, accruing signal transduction model was formulated to explain the observed MTT trend of conventional and ONP form. The model seems useful towards solving population specific varied results of chemotherapeutic agents. According to the model, MN10 and MN30 derivatives have good pharmacodynamics inertia and therefore, both the molecules were able to provide dose-dependent cytotoxic results.  相似文献   

    

《Computational Biology and Chemistry》2019

Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent of cost-effective and advanced sequencing techniques. To manage the pace of annotation with that of data generation, there is a shift to computational approaches which are based on homology, sequence and structure-based features, protein-protein interaction networks, phylogenetic profiles, and physicochemical properties, etc. A combination of these features has proven to be promising for protein function prediction in terms of improving prediction accuracy. In the present work, we have employed a combination of features based on sequence, physicochemical property, subsequence and annotation features with a total of 9890 features extracted and/or calculated for 171,212 reviewed prokaryotic proteins of 9 bacterial phyla from UniProtKB, to train a supervised deep learning ensemble model with the aim to categorize a bacterial hypothetical/unreviewed protein’s function into 1739 GO terms as functional classes. The proposed system being fully dedicated to bacterial organisms is a novel attempt amongst various existing machine learning based protein function prediction systems based on mixed organisms. Experimental results demonstrate the success of the proposed deep learning ensemble model based on deep neural network method with F1 measure of 0.7912 on the prepared Test dataset 1 of reviewed proteins.  相似文献   

    

Jiaqi Chen  Zhijun Tan  Haiyan Wu  Jixing Peng  Yuxiu Zhai  Mengmeng Guo 《Journal of separation science》2019,42(7):1423-1431

Okadaic acid is a marine biotoxin that primarily occurs in shellfish and can cause diarrheic shellfish poisoning in humans. When analyzing biological samples using liquid chromatography with tandem mass spectrometry, the presence of complex matrices is a major issue. Thus, it is crucial to selectively and simply extract the target analyte from samples and minimize matrix effects simultaneously. To meet this need, an immunomagnetic‐bead‐based liquid chromatography with tandem mass spectrometry method was developed to detect okadaic acid in shellfish. Magnetic beads bound to monoclonal antibody against okadaic acid were used as affinity probes to specifically enrich okadaic acid in samples, which effectively eliminated matrix effects. A magnetic separator was used to aggregate and separate magnetic particles from sample matrices, and methanol was used to elute okadaic acid from the magnetic beads. Standard solution prepared with methanol was employed directly for quantitative analysis. Several experimental conditions were optimized to improve performance. The method is of interest as a rapid (10 min) sample clean‐up and selective enrichment tool, and it showed good linearity and sensitivity, with reported limits of detection and quantitation of 3 and 10 μg/kg, respectively. Fifty‐three shellfish samples from an aquatic products market were tested using this method, and four samples positive for okadaic acid were found.  相似文献   

    

Xiaojuan Deng  Wenbin Li  Guosheng Ding  Tao Xue  Xiaoping Chen 《Separation & Purification Reviews》2019,48(1):14-29

Efficient enantioselective separation is a challenging task due to the identical physical and chemical properties of enantiomers. Functionalized magnetic nanomaterials modified with chiral ligands on their surface possess both magnetic property and chiral recognition ability, and have demonstrated great potential in chiral discrimination. This review summarizes the applications of magnetic nanomaterials modified with various chiral selectors (e.g., β-cyclodextrins, polymers, proteins, amino acids and cellulose) in enantioselective separation. After proper preparation and modification, these functionalized magnetic nanomaterials are effective for enantioseparation. Therefore, enantioseparations based on functionalized magnetic nanomaterials are convenient, economical and effective.  相似文献   

    

Nicholas Flynn  Ashish Ranjan  Joshua D. Ramsey 《Macromolecular bioscience》2019,19(10)

Reactive oxygen species (ROS) forming enzymes are of significant interest as anticancer agents due to their potent cytotoxicity. A key challenge in their clinical translation is attaining site‐specific delivery and minimizing biodistribution to healthy tissues. Here, complexes composed of the ROS enzyme glucose oxidase (GOX), poly‐l ‐lysine‐grafted‐polyethylene glycol (PLL‐g‐PEG), and anti‐prostate specific membrane antigen (anti‐PSMA) monoclonal antibody are synthesized for localized delivery and uptake in prostate cancer cells. Formation of anti‐PSMA‐PLL‐g‐PEG/GOX results in nanoscale complexes ≈30 nm in diameter with a ζ‐potential of 6 mV. The anti‐PSMA‐PLL‐g‐PEG/GOX complexes show significant cytotoxicity (≈60% reduction in cell viability) against PSMA‐expressing LNCaP cells compared to unmodified GOX. Importantly, cytotoxicity in LNCaP cells occurrs concurrently with anti‐PSMA‐PLL‐g‐PEG/GOX uptake and increases in intracellular generation of ROS. These results demonstrate that cytotoxicity of ROS inducing enzymes can be enhanced by intracellular delivery compared to equivalent concentrations of free enzyme, providing a novel means for cancer therapy.  相似文献   

    

Pradipta Behera  Mrinmoy De 《化学:亚洲杂志》2019,14(4):553-560

Optical array‐based sensors are attractive candidates for the detection of various bio‐analytes due to their convenient fabrication and measurements. For array‐based sensors, multichannel arrays are more advantageous and used frequently in many electronic sensors. But most reported optically array based sensors are constructed on a single channel array. This difficulty is mainly instigated from the overlap in optical responses. In this report we have used nano‐graphene oxide (nGO) and suitable fluorophores as sensor elements to construct a multichannel sensor array for the detection of protein analytes. By using the optimized multichannel array we are able to detect different proteins and mixtures of proteins with 100 % classification accuracy at sub‐nanomolar concentration. This modified method expedites the sensing analysis as well as minimizes the use of both analyte and sensor elements in array‐based protein sensing. We have also used this system for the single channel array‐based sensing to compare the sensitivity and the efficacy of these two systems for other applications. This work demonstrated an intrinsic trade‐off associated with these two methods which may be necessary to balance for array‐based analyte detections.  相似文献   

    

Dr. Elizabeth A. Caselle  Jennifer H. Yoon  Sagar Bhattacharya  Joel J. L. Rempillo  Zsófia Lengyel  Dr. Areetha D'Souza  Dr. Yurii S. Moroz  Patricia L. Tolbert  Dr. Alexander N. Volkov  Prof. Dr. Marcello Forconi  Prof. Dr. Carlos A. Castañeda  Prof. Dr. Olga V. Makhlynets  Prof. Dr. Ivan V. Korendovych 《ChemCatChem》2019,11(5):1374-1374

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Dr. Yosephine Gumulya  Dr. Weiliang Huang  Stephlina A. D'Cunha  Katelyn E. Richards  Raine E. S. Thomson  Dr. Dominic J. B. Hunter  Jong-Min Baek  Kurt L. Harris  Dr. M. Boden  Dr. James J. De Voss  Dr. Martin A. Hayes  Dr. Emre M. Isin  Dr. Shalini Andersson  Dr. Ulrik Jurva  Dr. Elizabeth M. J. Gillam 《ChemCatChem》2019,11(2):841-850

The structure of metabolites of drug candidates must frequently be characterised during drug discovery and development. However, synthesising metabolites with the correct stereoselective modifications can be challenging for chemically complex parent compounds. Biocatalysis using human drug-metabolising enzymes, such as cytochrome P450 2D6 (CYP2D6) is an alternative to chemical synthesis. However, most natural enzymes are unstable and have poor efficiency, limiting yields in preparative biotransformations. The aim of this study was to develop a library of robust mutant CYP2D enzymes for biocatalysis. The CLADE (combinatorial libraries of ancestors for directed evolution) approach increased the stability of CYP2D mutants obtained by DNA shuffling using three extant CYP2D forms. The resulting mutants showed divergent profiles of activity towards typical CYP2D substrates and included thermostable forms that may be useful for the further evolution of biocatalysts for specific applications.  相似文献   

    

Dr. Elizabeth A. Caselle  Jennifer H. Yoon  Sagar Bhattacharya  Joel J. L. Rempillo  Zsófia Lengyel  Dr. Areetha D'Souza  Dr. Yurii S. Moroz  Patricia L. Tolbert  Dr. Alexander N. Volkov  Prof. Dr. Marcello Forconi  Prof. Dr. Carlos A. Castañeda  Prof. Dr. Olga V. Makhlynets  Prof. Dr. Ivan V. Korendovych 《ChemCatChem》2019,11(5):1425-1430

Minimalist enzymes designed to catalyze model reactions provide useful starting points for creating catalysts for practically important chemical transformations. We have shown that Kemp eliminases of the AlleyCat family facilitate conversion of leflunomide (an immunosuppressor pro-drug) to its active form teriflunomide with outstanding rate enhancement (nearly four orders of magnitude) and catalytic proficiency (more than seven orders of magnitude) without any additional optimization. This remarkable activity is achieved by properly positioning the substrate in close proximity to the catalytic glutamate with very high pK_a.  相似文献