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https://www.readbyqxmd.com/read/28432857/on-the-importance-of-intramolecular-hydrogen-bond-cooperativity-in-d-glucose-an-nmr-and-qtaim-approach
#1
John S Lomas, Laurent Joubert
The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of D-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules...
April 22, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28432092/a-genome-wide-investigation-on-biofilm-formation-in-bacillus-cereus
#2
Fang Yan, Yiyang Yu, Kevin Gozzi, Yun Chen, Jian-Hua Guo, Yunrong Chai
Bacillus cereus is a soil-dwelling Gram-positive bacterium capable of forming structured multicellular communities, or biofilms. However, the regulatory pathways controlling biofilm formation are less well understood in B. cereus In this work, we developed a method to study B. cereus biofilms formed at the air-liquid interface. We applied two genome-wide approaches, random transposon insertion mutagenesis to identify genes that are potentially important for biofilm formation, and transcriptome analyses by RNA-seq to characterize genes that are differentially expressed in B...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431342/discovery-of-tetrahydrocarbazoles-as-dual-perk-and-prb-inhibitors
#3
Mahesh R Kulkarni, Madhav S Mane, Usha Ghosh, Rajiv Sharma, Nitin P Lad, Ankita Srivastava, Asha Kulkarni-Almeida, Prashant S Kharkar, Vijay M Khedkar, Shivaji S Pandit
The extracellular signal-regulated kinase (ERK) is one of the most important molecular targets for cancer that controls diverse cellular processes such as proliferation, survival, differentiation and motility. Similarly, the Rb (retinoblastoma protein) is a tumor suppressor protein and its function is to prevent excessive cell growth by inhibiting cell cycle progression. When the cell is ready to divide, pRb is phosphorylated, becomes inactive and allows cell cycle progression. Herein, we discovered a new series of tetrahydrocarbazoles as dual inhibitors of pERK and pRb phosphorylation...
March 2, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#4
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430982/evidence-of-nuclei-encoded-spliceosome-mediating-splicing-of-mitochondrial-rna
#5
Roberto H Herai, Priscilla D Negraes, Alysson R Muotri
Mitochondria are thought to have originated as free-living prokaryotes. Mitochondria organelles have small circular genomes with substantial structural (absence of histones and introns) and genetic similarity to bacteria. Contrary to the prevailing concept of intronless mitochondria, here we present evidences that mitochondrial RNA transcripts (mtRNA) are not limited to policystronic molecules, but also processed as nuclei-like transcripts that are differentially spliced and expressed in a cell-type specific manner...
April 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28430444/molecular-structuring-and-percolation-transition-in-hydrated-sulfonated-poly-ether-ether-ketone-membranes
#6
Madhusmita Tripathy, Sunil Kumar P B, Abhijit P Deshpande
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels($\lambda$: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#7
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta Energy Function, REF15...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28429938/high-resolution-accurate-mass-mass-spectrometry-enables-in-depth-characterization-of-in-vivo-biotransformations-for-intact-antibody-drug-conjugates
#8
Jintang He, Dian Su, Carl K Ng, Luna Liu, Shang-Fan Yu, Thomas H Pillow, Geoffrey Del Rosario, Martine Darwish, Byoung-Chul Lee, Rachana Ohri, Hongxiang Zhou, Xueji Wang, Jiawei Lu, Surinder Kaur, Keyang Xu
Antibody-drug conjugates (ADCs) represent a promising class of therapeutics for the targeted delivery of highly potent cytotoxic drugs to tumor cells to improve bioactivity while minimizing side effects. ADCs are composed of both small and large molecules, and therefore have complex molecular structures. In vivo biotransformations may further increase the complexity of ADCs, representing a unique challenge for bioanalytical assays. Quadrupole time-of-flight mass spectrometry (Q-TOF MS) with electrospray ionization has been widely used for characterization of intact ADCs...
April 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28429811/synthesis-and-structural-characterisation-of-the-aggregates-of-benzo-1-2-chalcogenazole-2-oxides
#9
Peter C Ho, Jamal Rafique, Jiwon Lee, Lucia M Lee, Hilary A Jenkins, James F Britten, Antonio L Braga, Ignacio Vargas-Baca
Iodine oxidation of bis[2-(hydroxyiminomethyl)phenyl] dichalcogenides yields benzo-1,2-chalcogenazole 2-oxides. Annulated derivatives of iso-tellurazole N-oxides spontaneously aggregate into cyclic tetra- and hexamers through TeO chalcogen bonding; the structures of the co-crystals with benzene and CH2Cl2 illustrate the ability of these macrocycles to interact with small guest molecules. The selenium congener crystallizes forming a supramolecular polymer. VT NMR indicates that both compounds aggregate in solution but only at low temperature in the selenium case...
April 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28428246/key-features-of-an-hsp70-chaperone-allosteric-landscape-revealed-by-ion-mobility-native-mass-spectrometry-and-double-electron-electron-resonance
#10
Alex L Lai, Eugenia M Clerico, Mandy E Blackburn, Nisha A Patel, Carol V Robinson, Peter P Borbat, Jack H Freed, Lila M Gierasch
Proteins are dynamic entities that populate conformational ensembles, and most functions of proteins depend on their dynamic character. Allostery, in particular, relies on ligand-modulated shifts in these conformational ensembles. Hsp70s are allosteric molecular chaperones with conformational landscapes that involve large rearrangements of their two domains (viz, the nucleotide-binding domain and substrate-binding domain) in response to adenine nucleotides and substrates. However, it remains unclear how the Hsp70 conformational ensemble is populated at each point of the allosteric cycle and how ligands control these populations...
April 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28428090/preparation-and-characterization-of-lipid-nanoparticle-pdna-complexes-for-stat3-downregulation-and-overcoming-chemotherapy-resistance-in-lung-cancer-cells
#11
Mustafa Kotmakçı, Vildan Bozok Çetintaş, A Gülten Kantarcı
Developments in the field of molecular oncology have revealed that resistance to chemotherapeutics is acqured through several mechanisms including overexpression of common oncogenic proteins. Signal Transducer and Activator of Transcription 3 (STAT3) is one of these oncogenes that is overexpressed in many cancer types. RNA interference (RNAi) is proven powerful tool for downregulating STAT3, allowing re-sensitization of resistant cancer cells. However, delivery of RNA interference-mediating molecules for STAT3 downregulation in lung cancer cells is limited to a small number of studies most of which employ commercially available transfection kits...
April 17, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28427622/efficient-removal-of-crystal-violet-and-methylene-blue-from-wastewater-by-ultrasound-nanoparticles-cu-mof-in-comparison-with-mechanosynthesis-method
#12
Amir Reza Abbasi, Maryam Karimi, Kim Daasbjerg
The present investigation reports the synthesis of CuBTC (BTC=1,3,5-benzenetricarboxylate) metal-organic frameworks (MOFs) under solid-state conditions and ultrasound irradiation. Herein, we study uptake and release properties of crystal violet (CV) and methylene blue (MB) from ultrasound nano-CuBTC MOF in comparison with mechanosynthesis method (bulk structure). The ultrasound-assisted methods give a decrease in the surface area as calculated from the reduced nitrogen adsorption capability. In comparison, the uptake of guest molecules on ultrasound nano-CuBTC is remarkable and clearly exceeds that of bulk structure in the aqueous solution of guests...
July 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28427249/crystal-structure-of-the-regulatory-domain-of-aphb-from-vibrio-vulnificus-a-virulence-gene-regulator
#13
Nohra Park, Saemee Song, Garam Choi, Kyung Ku Jang, Inseong Jo, Sang Ho Choi, Nam-Chul Ha
The transcriptional activator AphB has been implicated in acid resistance and pathogenesis in the food borne pathogens Vibrio vulnificus and Vibrio cholerae. To date, the full-length AphB crystal structure of V. cholerae has been determined and characterized by a tetrameric assembly of AphB consisting of a DNA binding domain and a regulatory domain (RD). Although acidic pH and low oxygen tension might be involved in the activation of AphB, it remains unknown which ligand or stimulus activates AphB at the molecular level...
April 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28426652/cheminformatics-aided-discovery-of-small-molecule-protein-protein-interaction-ppi-dual-inhibitors-of-tumor-necrosis-factor-tnf-and-receptor-activator-of-nf-%C3%AE%C2%BAb-ligand-rankl
#14
Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28425525/exploiting-hydrogen-bonding-interactions-to-probe-smaller-linear-and-cyclic-diamines-binding-to-g-quadruplexes-a-dft-and-molecular-dynamics-study
#15
Mrinal Kanti Si, Anik Sen, Bishwajit Ganguly
G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves...
April 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28425481/differences-in-salicylic-acid-glucose-conjugations-by-ugt74f1-and-ugt74f2-from-arabidopsis-thaliana
#16
Alayna M George Thompson, Cristina V Iancu, Kenneth E Neet, John V Dean, Jun-Yong Choe
Salicylic acid (SA) is a signaling molecule utilized by plants in response to various stresses. Through conjugation with small organic molecules such as glucose, an inactive form of SA is generated which can be transported into and stored in plant vacuoles. In the model organism Arabidopsis thaliana, SA glucose conjugates are formed by two homologous enzymes (UGT74F1 and UGT74F2) that transfer glucose from UDP-glucose to SA. Despite being 77% identical and with conserved active site residues, these enzymes catalyze the formation of different products: UGT74F1 forms salicylic acid glucoside (SAG), while UGT74F2 forms primarily salicylic acid glucose ester (SGE)...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425464/metabolic-labelling-of-the-carbohydrate-core-in-bacterial-peptidoglycan-and-its-applications
#17
Hai Liang, Kristen E DeMeester, Ching-Wen Hou, Michelle A Parent, Jeffrey L Caplan, Catherine L Grimes
Bacterial cells are surrounded by a polymer known as peptidoglycan (PG), which protects the cell from changes in osmotic pressure and small molecule insults. A component of this material, N-acetyl-muramic acid (NAM), serves as a core structural element for innate immune recognition of PG fragments. We report the synthesis of modifiable NAM carbohydrate derivatives and the installation of these building blocks into the backbone of Gram-positive and Gram-negative bacterial PG utilizing metabolic cell wall recycling and biosynthetic machineries...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28425184/enantioselective-synthesis-of-mitomycin%C3%A2-k-by-a-palladium-catalyzed-oxidative-tandem-cyclization
#18
Qiang-Shuai Gu, Dan Yang
The mitomycins, a family of bioactive natural products, feature a compact 6/5/5-fused polycyclic ring structure densely decorated with highly reactive and/or fragile quinone, amino ketal, and aziridine as well as carbamate moieties. It is this striking feature that has defeated numerous synthetic attempts towards these apparently small molecules, rendering them one of the most formidable targets for total synthesis. We herein report the first enantioselective synthesis of (+)-mitomycin K, a representative of G series mitomycins...
April 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28424620/relations-between-effects-and-structure-of-small-bicyclic-molecules-on-the-complex-model-system-saccharomyces-cerevisiae
#19
Matteo Brilli, Andrea Trabocchi, Tobias Weil, Duccio Cavalieri, Irene Stefanini
The development of compounds able to modify biological functions largely took advantage of parallel synthesis to generate a broad chemical variance of compounds to be tested for the desired effect(s). The budding yeast Saccharomyces cerevisiae is a model for pharmacological studies since a long time as it represents a relatively simple system to explore the relations among chemical variance and bioactivity. To identify relations between the chemical features of the molecules and their activity, we delved into the effects of a library of small compounds on the viability of a set of S...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28423958/strategies-and-perspectives-of-assembling-multi-enzyme-systems
#20
Shi-Zhen Wang, Yong-Hui Zhang, Hong Ren, Ya-Li Wang, Wei Jiang, Bai-Shan Fang
Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein...
April 20, 2017: Critical Reviews in Biotechnology
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