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Biological Chemistry

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https://www.readbyqxmd.com/read/29342358/synthesis-and-biological-characterization-of-aryl-uracil-inhibitors-of-hepatitis-c-virus-ns5b-polymerase-discovery-of-abt-072-a-trans-stilbene-analog-with-good-oral-bioavailability
#1
John Randolph, A Chris Krueger, Pamela Donner, John K Pratt, Dachun Liu, Christopher E Motter, Todd W Rockway, Mike D Tufano, Rolf Wagner, Hock B Lim, Jill M Beyer, Rubina Mondal, Neeta S Panchal, Lynn Colletti, Yaya Liu, Gennadiy Koev, Warren M Kati, Lisa E Hernandez, David W A Beno, Kenton L Longenecker, Kent D Stewart, Emily O Dumas, Akhteruzzaman Molla, Clarence Maring
ABT-072 is a non-nucleoside HCV NS5B polymerase inhibitor that was discovered as part of a program to identify new direct-acting antivirals (DAAs) for the treatment of HCV infection. This compound was identified during a medicinal chemistry effort to improve on an original lead, inhibitor 1, which we described in a previous publication. Replacement of the amide linkage in 1 with a trans-olefin resulted in improved compound permeability and solubility, and provided much better pharmacokinetic properties in preclinical species...
January 17, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29341592/application-of-decafluorobiphenyl-dfbp-moiety-as-a-linker-in-bioconjugation
#2
Fernando Albericio, Saba Alapour, Beatriz G de la Torre, Deresh Ramjugernath, Neil Anthony Koorbanally
Considerable attention has been devoted to fluorinated compounds due to their unique and interesting properties. Many modern pharmaceuticals contain fluorinated substituents, which are commonly synthesized using selective fluorinating reagents. Decafluorobiphenyl (DFBP) as a fluorinated linker is susceptible to nucleophilic attack. This nucleophilic reaction has been widely studied using various nucleophiles. Sulfur and nitrogen containing nucleophiles have been of particular interest, especially in bioconjugated reactions...
January 17, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29341307/chemical-and-enzymatic-strategies-for-bacterial-and-mammalian-cell-surface-engineering
#3
Xiaobao Bi, Juan Yin, Ashley Chen Guanbang, Chuan-Fa Liu
Cell surface serves important functions such as the regulation of cell-cell and cell-environment interactions. The understanding and manipulation of the cell surface is important for a wide range of fundamental studies of cellular behavior and for biotechnological and medical applications. With the rapid advance of biology, chemistry and materials science, many strategies have been developed for the functionalization of bacterial and mammalian cell surfaces. Here, we review the recent development of chemical and enzymatic approaches to cell surface engineering with particular emphasis on discussing the advantages and limitations of each of these strategies...
January 17, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29340616/pychimera-use-ucsf-chimera-modules-in-any-python-2-7-project
#4
Jaime Rodríguez-Guerra Pedregal, Jean-Didier Maréchal
Motivation: UCSF Chimera (Pettersen et al., 2004) is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C ++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera's arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX (Goddard et al...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340362/synergetic-topography-and-chemistry-cues-guiding-osteogenic-differentiation-in-bone-marrow-stromal-cells-through-erk1-2-and-p38-mapk-signaling-pathway
#5
Xinran Zhang, Haotian Li, Chucheng Lin, Congqin Ning, Kaili Lin
Both the topographic surface and chemical composition modification can enhance rapid osteogenic differentiation and bone formation. Till now, the synergetic effects of topography and chemistry cues guiding biological responses have been rarely reported. Herein, the ordered micro-patterned topography and classically essential trace element of strontium (Sr) ion doping were selected to imitate topography and chemistry cues, respectively. The ordered micro-patterned topography on Sr ion-doped bioceramics was successfully duplicated using the nylon sieve as the template...
January 17, 2018: Biomaterials Science
https://www.readbyqxmd.com/read/29340006/the-impact-of-the-progressive-efficiency-test-on-a-rowing-ergometer-on-white-blood-cells-distribution-and-clinical-chemistry-changes-in-paralympic-rowers-during-the-preparatory-stage-before-the-paralympic-games-in-rio-2016-a-case-report
#6
Robert Nowak, Rafał Buryta, Krzysztof Krupecki, Tomasz Zając, Marek Zawartka, Patrizia Proia, Dorota Kostrzewa-Nowak
There is a large gap in knowledge regarding research on post-exercise blood changes in disabled athletes. There are relatively few data on adaptive mechanisms to exercise in disabled athletes, including disabled rowers. Two rowers from a Polish adaptive rowing settle TAMix2x that qualified for the Paralympic Games in Rio, 2016 took part in this study. They performed a progressive test on a rowing ergometer until exhaustion. The cardiorespiratory fitness measures, complete blood count, white blood cells' distribution and 30 clinical chemistry variables describing laboratory diagnostic profiles and general health were determined...
December 2017: Journal of Human Kinetics
https://www.readbyqxmd.com/read/29339554/synthetic-biology-strategies-for-improving-microbial-synthesis-of-green-biopolymers
#7
Lisa A Anderson, M Ahsanul Islam, Kristala L J Prather
Polysaccharide-based biopolymers have many material properties relevant to industrial and medical uses, including as drug delivery agents, wound healing adhesives, and food additives and stabilizers. Traditionally, polysaccharides are obtained from natural sources. Microbial synthesis offers an attractive alternative for sustainable production of tailored biopolymers. Here, we review synthetic biology strategies for select "green" biopolymers: cellulose, alginate, chitin, chitosan, and hyaluronan. Microbial production pathways, opportunities for pathway yield improvements, and advances in microbial engineering of biopolymers in various hosts are discussed...
January 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29337878/tetrasubstituted-imidazolium-salts-as-potent-antiparasitic-agents-against-african-and-american-trypanosomiases
#8
Ouldouz Ghashghaei, Nicola Kielland, Marc Revés, Martin C Taylor, John M Kelly, Ornella Di Pietro, Diego Muñoz-Torrero, Belén Pérez, Rodolfo Lavilla
Imidazolium salts are privileged compounds in organic chemistry, and have valuable biological properties. Recent studies show that symmetric imidazolium salts with bulky moieties can display antiparasitic activity against T. cruzi. After developing a facile methodology for the synthesis of tetrasubstituted imidazolium salts from propargylamines and isocyanides, we screened a small library of these adducts against the causative agents of African and American trypanosomiases. These compounds display nanomolar activity against T...
January 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29337573/cryoprotectants-severely-exacerbate-x-ray-induced-photoreduction
#9
Kurt H Nienaber, M Jake Pushie, Julien J H Cotelesage, Ingrid J Pickering, Graham N George
Approximately 11% of enzymes contain a transition metal ion that is essential for catalytic function. Such metalloenzymes catalyze much of the most chemically challenging and biologically essential chemistry carried out by life. X-ray based methods, predominantly macromolecular crystallography (MX) and also X-ray absorption spectroscopy (XAS), have proved essential for determining structures of transition metal ion-containing active sites in order to deduce enzyme catalytic mechanisms. However, X-ray irradiation can induce change in both oxidation state and structure of the metal, which is problematic in structure determination...
January 16, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29336493/n-terminal-cu-binding-motifs-xxx-zzz-his-atcun-and-xxx-his-and-their-derivatives-chemistry-biology-and-medicinal-applications
#10
Peter Faller, Paulina Gonzalez, Karolina Bossak, Ewelina Stefaniak, Christelle Hureau, Laurent Raibaut, Wojciech Bal
Peptides and proteins with N-terminal amino acid sequences NH2-Xxx-His (XH) and NH2-Xxx-Zzz-His (XZH) form well established high affinity CuII-complexes. Key examples are Asp-Ala-His (in serum albumin) and Gly-His-Lys, the wound healing factor. This opens a straightforward way to add a high affinity CuII-binding site to almost any peptide or protein, by chemical or recombinant approaches. Thus, these motifs, NH2-Xxx-Zzz-His in particular, have been used to equip peptides and proteins with a multitude of functions based on the redox activity of Cu, including nuclease, protease, glycosidase, or oxygen activation, useful in anticancer or antimicrobial drugs...
January 16, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29335694/the-seventh-biennial-berry-health-benefits-symposium
#11
EDITORIAL
Navindra P Seeram, Britt Burton-Freeman
Research advancing current scientific understanding of the health benefits of berries continues to increase. The Berry Health Benefits Symposium (BHBS) is a biennial meeting highlighting the most recent berry health benefits research from all over the world. Pismo Beach, California was the venue for the seventh biennial BHBS in 2017, and featured oral invited papers on heart health and healthy aging, gut/microbiome health, brain aging, inflammation, cancer prevention, berry special topics, technology and chemistry...
January 16, 2018: Food & Function
https://www.readbyqxmd.com/read/29335493/biophysical-feedbacks-mediate-carbonate-chemistry-in-coastal-ecosystems-across-spatiotemporal-gradients
#12
Nyssa J Silbiger, Cascade J B Sorte
Ocean acidification (OA) projections are primarily based on open ocean environments, despite the ecological importance of coastal systems in which carbonate dynamics are fundamentally different. Using temperate tide pools as a natural laboratory, we quantified the relative contribution of community composition, ecosystem metabolism, and physical attributes to spatiotemporal variability in carbonate chemistry. We found that biological processes were the primary drivers of local pH conditions. Specifically, non-encrusting producer-dominated systems had the highest and most variable pH environments and the highest production rates, patterns that were consistent across sites spanning 11° of latitude and encompassing multiple gradients of natural variability...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335424/functionalisation-of-detonation-nanodiamond-for-monodispersed-soluble-dna-nanodiamond-conjugates-using-mixed-silane-bead-assisted-sonication-disintegration
#13
Robert Edgington, Katelyn M Spillane, George Papageorgiou, William Wray, Hitoshi Ishiwata, Mariana Labarca, Sergio Leal-Ortiz, Gordon Reid, Martin Webb, John Foord, Nicholas Melosh, Andreas T Schaefer
Nanodiamonds have many attractive properties that make them suitable for a range of biological applications, but their practical use has been limited because nanodiamond conjugates tend to aggregate in solution during or after functionalisation. Here we demonstrate the production of DNA-detonation nanodiamond (DNA-DND) conjugates with high dispersion and solubility using an ultrasonic, mixed-silanization chemistry protocol based on the in situ Bead-Assisted Sonication Disintegration (BASD) silanization method...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334758/anticancer-thiosemicarbazones-chemical-properties-interaction-with-iron-metabolism-and-resistance-development
#14
Petra Heffeter, Veronika F S Pape, Eva A Enyedy, Bernhard K Keppler, Gergely Szakas, Christian R Kowol
SIGNIFICANCE: During the last decades, thiosemicarbazones have been clinically developed for a variety of diseases including tuberculosis, viral infections, malaria and cancer. With regard to malignant diseases, the class of α-N-heterocyclic thiosemicarbazones, and here especially Triapine, was intensively developed in multiple clinical phase I/II trials. Recent Advances: Very recently two new derivatives, namely COTI-2 and DpC have entered phase I evaluation. Based on the strong metal-chelating/metal-interacting properties of thiosemicarbazones, interference with the cellular iron (and copper) homeostasis is assumed to play an important role in their biological activity...
January 15, 2018: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29333473/charge-migration-and-charge-transfer-in-molecular-systems
#15
REVIEW
Hans Jakob Wörner, Christopher A Arrell, Natalie Banerji, Andrea Cannizzo, Majed Chergui, Akshaya K Das, Peter Hamm, Ursula Keller, Peter M Kraus, Elisa Liberatore, Pablo Lopez-Tarifa, Matteo Lucchini, Markus Meuwly, Chris Milne, Jacques-E Moser, Ursula Rothlisberger, Grigory Smolentsev, Joël Teuscher, Jeroen A van Bokhoven, Oliver Wenger
The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer...
November 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/29332833/a-combination-of-thiol-ene-click-chemistry-and-surface-initiated-atom-transfer-radical-polymerization-fabrication-of-boronic-acid-functionalized-magnetic-graphene-oxide-composite-for-enrichment-of-glycoproteins
#16
Jie Su, Xiwen He, Langxing Chen, Yukui Zhang
An efficient glycoproteins enrichment platform is one of vital preprocessing steps in biomarker research and in particular glycoproteomics. In this work, a well-defined boronic acid functionalized magnetic graphene oxide nanocomposite (Fe3O4-GO@PAAPBA) was synthesized for the selective enrichment of glycoproteins from complex biological samples via a novel strategy based on the "thiol-ene" click chemistry and surface initiated atom transfer radical polymerization (SI-ATRP). The initiator of ATRP was anchored to the surface of substrate through "thiol-ene" click reaction...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29329334/ensemble-learning-method-for-the-prediction-of-new-bioactive-molecules
#17
Lateefat Temitope Afolabi, Faisal Saeed, Haslinda Hashim, Olutomilayo Olayemi Petinrin
Pharmacologically active molecules can provide remedies for a range of different illnesses and infections. Therefore, the search for such bioactive molecules has been an enduring mission. As such, there is a need to employ a more suitable, reliable, and robust classification method for enhancing the prediction of the existence of new bioactive molecules. In this paper, we adopt a recently developed combination of different boosting methods (Adaboost) for the prediction of new bioactive molecules. We conducted the research experiments utilizing the widely used MDL Drug Data Report (MDDR) database...
2018: PloS One
https://www.readbyqxmd.com/read/29328784/dna-encoded-chemical-libraries-a-selection-system-based-on-endowing-organic-compounds-with-amplifiable-information
#18
Dario Neri, Richard A Lerner
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice...
January 12, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29328673/fluorescent-proteins-detect-host-structural-rearrangements-via-electrostatic-mechanism
#19
Lena Simine, Heiko Lammert, Li Sun, Jose Nelson Onuchic, Peter J Rossky
The rational design of genetically encoded fluorescent bio-sensors, which can detect rearrangements of target proteins via interdomain allostery, is hindered by the absence of mechanistic understanding of the underlying photo-physics. Here, we focus on the modulation of fluorescence by mechanical perturbation in a popular biological probe: enhanced Green Fluorescent Protein (eGFP). Using a combination of molecular dynamics (MD) simulations and quantum chemistry, and a set of physically motivated assumptions, we construct a map of fluorescence quantum yield as a function of a 2D electric field imposed by the protein environment on the fluorophore...
January 12, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29328627/effect-of-surface-chemistry-and-associated-protein-corona-on-the-long-term-biodegradation-of-iron-oxide-nanoparticles-in-vivo
#20
Grazyna Stepien, María Moros, Marta Perez-Hernandez, Marta Monge, Lucía Gutiérrez, Raluca Maria M Fratila, Marcelo Las Heras, Sebastian Menao Guillen, Juan Jose Puente Lanzarote, Conxita Solans, Julián Pardo, Jesús M De La Fuente
Protein corona formed on the surface of nanoparticle in biological medium determines its behavior in vivo. Here, iron oxide nanoparticles containing the same core and shell, but bearing two different surface coatings, either glucose or poly(ethylene glycol), were evaluated. The nanoparticles protein adsorption, in vitro degradation, and in vivo biodistribution and biotransformation over four months, were investigated. Although both types of nanoparticles bound a similar amount of proteins in vitro, the differences in the protein corona composition correlated to the nanoparticles biodistribution in vivo...
January 12, 2018: ACS Applied Materials & Interfaces
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