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Homology modelling

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https://www.readbyqxmd.com/read/28346871/synthesis-in-vitro-evaluation-and-molecular-docking-studies-of-novel-amide-linked-triazolyl-glycoconjugates-as-new-inhibitors-of-%C3%AE-glucosidase
#1
Shyam Ji Gupta, Samrat Dutta, Rahul L Gajbhiye, Parasuraman Jaisankar, Asish Kumar Sen
A series of N-substituted amide linked triazolyl β-d-glucopyranoside derivatives (4a-l) were synthesized and their in vitro inhibitory activity against yeast α-glucosidase enzyme [EC.3.2.1.20] was assessed. Compounds 4e (IC50=156.06μM), 4f (IC50=147.94μM), 4k (IC50=127.71μM) and 4l (IC50=121.33μM) were identified as the most potent inhibitors for α-glucosidase as compared to acarbose (IC50=130.98μM) under the same in vitro experimental conditions. Kinetic study showed that both 4e and 4f inhibit the enzyme in a competitive manner with p-nitrophenyl α-d-glucopyranoside as substrate...
March 18, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28346135/polo-like-kinase-dependent-phosphorylation-of-the-synaptonemal-complex-protein-syp-4-regulates-double-strand-break-formation-through-a-negative-feedback-loop
#2
Saravanapriah Nadarajan, Talley J Lambert, Elisabeth Altendorfer, Jinmin Gao, Michael D Blower, Jennifer C Waters, Monica P Colaiácovo
The synaptonemal complex (SC) is an ultrastructurally conserved proteinaceous structure that holds homologous chromosomes together and is required for the stabilization of pairing interactions and the completion of crossover (CO) formation between homologs during meiosis I. Here, we identify a novel role for a central region component of the SC, SYP-4, in negatively regulating formation of recombination-initiating double-strand breaks (DSBs) via a feedback loop triggered by crossover designation in C. elegans...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28345667/the-toxicity-of-angiotensin-converting-enzyme-inhibitors-to-larvae-of-the-disease-vectors-aedes-aegypti-and-anopheles-gambiae
#3
Zatul-'Iffah Abu Hasan, Helen Williams, Nur M Ismail, Hidayatulfathi Othman, Gyles E Cozier, K Ravi Acharya, R Elwyn Isaac
The control of mosquitoes is threatened by the appearance of insecticide resistance and therefore new control chemicals are urgently required. Here we show that inhibitors of mosquito peptidyl dipeptidase, a peptidase related to mammalian angiotensin-converting enzyme (ACE), are insecticidal to larvae of the mosquitoes, Aedes aegypti and Anopheles gambiae. ACE inhibitors (captopril, fosinopril and fosinoprilat) and two peptides (trypsin-modulating oostatic factor/TMOF and a bradykinin-potentiating peptide, BPP-12b) were all inhibitors of the larval ACE activity of both mosquitoes...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345004/homology-directed-recombination-for-enhanced-engineering-of-chimeric-antigen-receptor-t-cells
#4
Malika Hale, Baeckseung Lee, Yuchi Honaker, Wai-Hang Leung, Alexandra E Grier, Holly M Jacobs, Karen Sommer, Jaya Sahni, Shaun W Jackson, Andrew M Scharenberg, Alexander Astrakhan, David J Rawlings
Gene editing by homology-directed recombination (HDR) can be used to couple delivery of a therapeutic gene cassette with targeted genomic modifications to generate engineered human T cells with clinically useful profiles. Here, we explore the functionality of therapeutic cassettes delivered by these means and test the flexibility of this approach to clinically relevant alleles. Because CCR5-negative T cells are resistant to HIV-1 infection, CCR5-negative anti-CD19 chimeric antigen receptor (CAR) T cells could be used to treat patients with HIV-associated B cell malignancies...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344992/mechanism-of-deletion-removing-all-dystrophin-exons-in-a-canine-model-for-dmd-implicates-concerted-evolution-of-x-chromosome-pseudogenes
#5
D Jake VanBelzen, Alock S Malik, Paula S Henthorn, Joe N Kornegay, Hansell H Stedman
Duchenne muscular dystrophy (DMD) is a lethal, X-linked, muscle-wasting disorder caused by mutations in the large, 2.4-Mb dystrophin gene. The majority of DMD-causing mutations are sporadic, multi-exon, frameshifting deletions, with the potential for variable immunological tolerance to the dystrophin protein from patient to patient. While systemic gene therapy holds promise in the treatment of DMD, immune responses to vectors and transgenes must first be rigorously evaluated in informative preclinical models to ensure patient safety...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344646/comparative-insights-into-the-saccharification-potentials-of-a-relatively-unexplored-but-robust-penicillium-funiculosum-glycoside-hydrolase-7-cellobiohydrolase
#6
Funso Emmanuel Ogunmolu, Navya Bhatt Kammachi Jagadeesha, Rakesh Kumar, Pawan Kumar, Dinesh Gupta, Syed Shams Yazdani
BACKGROUND: GH7 cellobiohydrolases (CBH1) are vital for the breakdown of cellulose. We had previously observed the enzyme as the most dominant protein in the active cellulose-hydrolyzing secretome of the hypercellulolytic ascomycete-Penicillium funiculosum (NCIM1228). To understand its contributions to cellulosic biomass saccharification in comparison with GH7 cellobiohydrolase from the industrial workhorse-Trichoderma reesei, we natively purified and functionally characterized the only GH7 cellobiohydrolase identified and present in the genome of the fungus...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28343756/inhibition-of-malassezia-globosa-carbonic-anhydrase-with-phenols
#7
Yeganeh Entezari Heravi, Silvia Bua, Alessio Nocentini, Sonia Del Prete, Ali Akbar Saboury, Hassan Sereshti, Clemente Capasso, Paola Gratteri, Claudiu T Supuran
A panel of 22 phenols was investigated as inhibitors of the β-class carbonic anhydrase (CAs, EC 4.2.1.1) from the fungal parasite Malassezia globosa (MgCA), a validated anti-dandruff drug target. The displayed inhibitory activities were compared to the ones previously reported against the off-target widely distributed human (h) isoforms hCA I and II. All tested phenols possessed a better efficacy in inhibiting MgCA than the clinically used sulfonamide acetazolamide, with KIs in the range of 2.5 and 65.0μM...
March 18, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28341457/thyroid-hormone-transport-across-l-type-amino-acid-transporters-what-can-molecular-modelling-tell-us
#8
Gerd Krause, Katrin Manuela Hinz
Thyroid hormones (THs) and their derivatives require transmembrane transporters (TTs) to mediate their translocation across the cell membrane. Among these TTs, the L-type amino acid transporters (LAT) not only transport amino acids (AAs) but also certain THs and their derivatives. This review summarizes available knowledge concerning structure function patterns of the TH transport by LAT1 and LAT2. For example, LAT2 imports 3,3'-T2 and T3, but not rT3 and T4. In contrast to amino acids, THs are not at all exported by LAT2...
March 21, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#9
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28339850/allelic-variation-in-tlr4-is-linked-to-resistance-to-salmonella-enteritidis-infection-in-chickens
#10
Peng Li, Huihua Wang, Xingwang Zhao, Zhongyong Gou, Ranran Liu, Yongmei Song, Qinghe Li, Maiqing Zheng, Huanxian Cui, Nadia Everaert, Guiping Zhao, Jie Wen
Salmonella Enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Polymorphisms of the TLR4 gene may affect recognition by Toll-like receptor 4 (TLR4) of bacterial lipopolysaccharide (LPS), leading to differences in host resistance to pathogenic infections. The present study has investigated polymorphic loci of chicken TLR4 (ChTLR4) in ten chicken breeds, electrostatic potentials of mutant structures of TLR4, and a linkage analysis between allelic variation and survival ratio to infection with SE in specific-pathogen-free (SPF) White Leghorns...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339300/genetic-manipulation-by-zinc-finger-nucleases-in-rat-induced-pluripotent-stem-cells
#11
Sheng Yang, Shufang Ding, Qianhua Xu, Xiong Li, Qiong Xiong
Induced pluripotent stem cells (iPSCs) have an extensive application in regenerative medicine, pharmaceutical discovery, and basic research. With the recent derivation of rat iPSCs, it is now feasible to apply genetic manipulation in this species. But such tools do not yet exist for many rat strains, especially for disease model rat. The Sprague Dawley (SD) rat is an inbred disease model for hypertension, nephropathy, pulmonary hypertension, depression, and alcohol consumption. In this study, the SD rat iPSCs were generated using lentiviral method...
March 24, 2017: Cellular Reprogramming
https://www.readbyqxmd.com/read/28339035/duration-of-simulated-microgravity-affects-the-differentiation-of-mesenchymal-stem-cells
#12
Li Xue, Yaohui Li, Jun Chen
Previous evidence has suggested that physical microenvironments and mechanical stresses, independent of soluble factors, influence mesenchymal stem cell (MSC) fate. In the present study, simulated microgravity (SMG) was demonstrated to regulate the differentiation of mesenchymal stem cells. This may be a novel strategy for tissue engineering and regenerative medicine. Rat MSCs were cultured for 72 h or 10 days in either normal gravity or a clinostat to model microgravity, followed with culture in diverse differential media...
March 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28339030/increased-phosphorylation-of-4e%C3%A2-binding-protein-1-predicts-poor-prognosis-for-patients-with-colorectal-cancer
#13
Yufeng Miao, Lige Chen, Cuifen Shi, Rengen Fan, Ping Chen, Hongqi Liu, Aihua Xia, Haixin Qian
As demonstrated in previous studies, the phosphorylated form of 4E‑binding protein 1 (p‑4E‑BP1) may be a suitable tumor biomarker. The aim of the current study was to examine the expression status of p‑4E‑BP1 in colorectal cancer (CRC), in order to determine its clinical significance. The present study enrolled 89 patients with CRC that had undergone radical resection. Paired tumor and adjacent normal tissues were evaluated using immunohistochemistry to detect the protein expression of p‑4E‑BP1 and phosphatase and tensin homolog (PTEN)...
March 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28338736/microcompartmentation-of-cytosolic-aldolase-by-interaction-with-the-actin-cytoskeleton-in-arabidopsis
#14
Constantine Garagounis, Kalliopi-Ioanna Kostaki, Tim J Hawkins, Ian Cummins, Mark D Fricker, Patrick J Hussey, Alistair M Hetherington, Lee J Sweetlove
Evidence is accumulating for molecular microcompartments formed when proteins interact in localized domains with the cytoskeleton, organelle surfaces, and intracellular membranes. To understand the potential functional significance of protein microcompartmentation in plants, we studied the interaction of the glycolytic enzyme fructose bisphosphate aldolase with actin in Arabidopsis thaliana. Homology modelling of a major cytosolic isozyme of aldolase, FBA8, suggested that the tetrameric holoenzyme has two actin binding sites and could therefore act as an actin-bundling protein, as was reported for animal aldolases...
February 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338718/identification-and-characterization-of-gra6-gra7-of-neospora-caninum-in-mdbk-cells
#15
Jingquan Dong, Jianhua Li, Jinpeng Wang, Fei Li, Ju Yang, Pengtao Gong, He Li, Xichen Zhang
Neospora caninum, an apicomplexan parasite, is recognized as a major bovine abortifacient. Dense granule antigens (GRAs) play important roles in the formation and modification of parasitophorous vacuoles (PVs) in Toxoplasma gondii. However, a few studies investigating GRAs have been reported in N. caninum. The aim of the present study was to characterize the dense GRA6/GRA7 of N. caninum in PVs using MDBK cells as a host cell model. Neospora caninum was inoculated into MDBK cells, and changes were observed using a transmission electron microscope (TEM)...
February 24, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28337696/cerebral-dopamine-neurotrophic-factor-a-potential-therapeutic-agent-for-parkinson-s-disease
#16
REVIEW
Tingting Tang, Yong Li, Qian Jiao, Xixun Du, Hong Jiang
The application of neurotrophic factors (NTFs) is a promising therapeutic strategy for neurodegenerative disorders such as Parkinson's disease (PD). Many NTFs have been reported to enhance the survival, regeneration, and differentiation of neurons and to induce synaptic plasticity. However, because of their potential side-effects and low efficacy after clinical administration, more potent treatments for neurodegenerative disorders are being sought. Cerebral dopamine neurotrophic factor (CDNF), a newly-identified NTF homologous to mesencephalic astrocyte-derived NTF, is structurally and functionally different from other NTFs, providing new hope especially for PD patients...
March 23, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/28337556/homologous-gene-targeting-of-a-carotenoids-biosynthetic-gene-in-rhodosporidium-toruloides-by-agrobacterium-mediated-transformation
#17
Wenyi Sun, Xiaobing Yang, Xueying Wang, Xinping Lin, Yanan Wang, Sufang Zhang, Yushi Luan, Zongbao K Zhao
OBJECTIVES: To target a carotenoid biosynthetic gene in the oleaginous yeast Rhodosporidium toruloides by using the Agrobacterium-mediated transformation (AMT) method. RESULTS: The RHTO_04602 locus of R. toruloides NP11, previously assigned to code the carotenoid biosynthetic gene CRTI, was amplified from genomic DNA and cloned into the binary plasmid pZPK-mcs, resulting in pZPK-CRT. A HYG-expression cassette was inserted into the CRTI sequence of pZPK-CRT by utilizing the restriction-free clone strategy...
March 23, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28336515/the-motor-activity-of-dna2-functions-as-an-ssdna-translocase-to-promote-dna-end-resection
#18
Maryna Levikova, Cosimo Pinto, Petr Cejka
DNA2 nuclease-helicase functions in DNA replication and recombination. This requires the nuclease of DNA2, while, in contrast, the role of the helicase activity has been unclear. We now show that the motor activity of both recombinant yeast and human DNA2 promotes efficient degradation of long stretches of ssDNA, particularly in the presence of the replication protein A. This degradation is further stimulated by a direct interaction with a cognate RecQ family helicase, which functions with DNA2 in DNA end resection to initiate homologous recombination...
March 23, 2017: Genes & Development
https://www.readbyqxmd.com/read/28336429/insight-into-stereochemistry-of-a-new-imp-allelic-variant-imp-55-metallo-%C3%AE-lactamase-identified-in-a-clinical-strain-of-acinetobacter-baumannii
#19
Mohammad Reza Shakibaie, Omid Azizi, Fereshteh Shahcheraghi
Metallo-β-lactamases (MBLs) such as IMPs are broad-spectrum β-lactamases that inactivate virtually all β-lactam antibiotics including carbapenems. In this study, we investigated the hydrolytic activity, phylogenetic relationship, three dimensional (3D) structure including zinc binding motif of a new IMP variant (IMP-55) identified in a clinical strain of Acinetobacter baumannii (AB). AB strain 56 was isolated from an adult ICU of a teaching hospital in Kerman, Iran. It exhibited MIC 32μg/ml to imipenem and showed MBL activity...
March 20, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28334827/yeast-hrq1-shares-structural-and-functional-homology-with-the-disease-linked-human-recq4-helicase
#20
Cody M Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L Bochman
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops...
February 25, 2017: Nucleic Acids Research
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