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Small molecule structure

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https://www.readbyqxmd.com/read/28644899/new-insights-in-dehydration-stress-behavior-of-two-maize-hybrids-using-advanced-distributed-reactivity-model-drm-responses-to-the-impact-of-24-epibrassinolide
#1
Hadi Waisi, Bojan Janković, Marija Janković, Bogdan Nikolić, Ivica Dimkić, Blažo Lalević, Vera Raičević
Proposed distributed reactivity model of dehydration for seedling parts of two various maize hybrids (ZP434, ZP704) was established. Dehydration stresses were induced thermally, which is also accompanied by response of hybrids to heat stress. It was found that an increased value of activation energy counterparts within radicle dehydration of ZP434, with a high concentration of 24-epibrassinolide (24-EBL) at elevated operating temperatures, probably causes activation of diffusion mechanisms in cutin network and may increases likelihood of formation of free volumes, large enough to accommodate diffusing molecule...
2017: PloS One
https://www.readbyqxmd.com/read/28644618/exploring-new-assembly-modes-of-uranyl-terephthalate-templated-syntheses-and-structural-regulation-of-a-series-of-rare-2d-%C3%A2-3d-polycatenated-frameworks
#2
Lei Mei, Cong-Zhi Wang, Liu-Zheng Zhu, Zeng-Qiang Gao, Zhi-Fang Chai, John K Gibson, Wei-Qun Shi
The reaction of uranyl nitrate with terephthalic acid (H2TP) under hydrothermal conditions in the presence of an organic base, 1,3-(4,4'-bispyridyl)propane (BPP) or 4,4'-bipyridine (BPY), provided four uranyl terephthalate compounds with different entangled structures by a pH-tuning method. [UO2(TP)1.5](H2BPP)0.5·2H2O (1) obtained in a relatively acidic solution (final aqueous pH, 4.28) crystallizes in the form of a noninterpenetrated honeycomb-like two-dimensional network structure. An elevation of the solution pH (final pH, 5...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644406/an-updated-review-on-marine-anticancer-compounds-the-use-of-virtual-screening-for-the-discovery-of-small-molecule-cancer-drugs
#3
REVIEW
Verónica Ruiz-Torres, Jose Antonio Encinar, María Herranz-López, Almudena Pérez-Sánchez, Vicente Galiano, Enrique Barrajón-Catalán, Vicente Micol
Marine secondary metabolites are a promising source of unexploited drugs that have a wide structural diversity and have shown a variety of biological activities. These compounds are produced in response to the harsh and competitive conditions that occur in the marine environment. Invertebrates are considered to be among the groups with the richest biodiversity. To date, a significant number of marine natural products (MNPs) have been established as antineoplastic drugs. This review gives an overview of MNPs, both in research or clinical stages, from diverse organisms that were reported as being active or potentially active in cancer treatment in the past seventeen years (from January 2000 until April 2017) and describes their putative mechanisms of action...
June 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28644007/cyclotides-as-tools-in-chemical-biology
#4
Simon J de Veer, Joachim Weidmann, David J Craik
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28642839/the-mitochondrial-complex-i-ty-of-cancer
#5
REVIEW
Félix A Urra, Felipe Muñoz, Alenka Lovy, César Cárdenas
Recent evidence highlights that the cancer cell energy requirements vary greatly from normal cells and that cancer cells exhibit different metabolic phenotypes with variable participation of both glycolysis and oxidative phosphorylation. NADH-ubiquinone oxidoreductase (Complex I) is the largest complex of the mitochondrial electron transport chain and contributes about 40% of the proton motive force required for mitochondrial ATP synthesis. In addition, Complex I plays an essential role in biosynthesis and redox control during proliferation, resistance to cell death, and metastasis of cancer cells...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28642545/high-throughput-screening-of-small-molecule-inhibitors-of-the-streptococcus-quorum-sensing-signal-pathway
#6
Seiji Ishii, Kenji Fukui, Satoshi Yokoshima, Kazuo Kumagai, Youko Beniyama, Tetsuya Kodama, Tohru Fukuyama, Takayoshi Okabe, Tetsuo Nagano, Hirotatsu Kojima, Takato Yano
The main components of the quorum-sensing system are expected to be favorable targets for drug development to combat various chronic infectious diseases. ComA of Streptococcus is an ATP-binding cassette transporter containing a peptidase domain (PEP), which is essential for the quorum-sensing signal production. Using high-throughput screening, we found a potent small molecule that suppressed the S. mutans quorum-sensing pathway through inhibition of PEP activity. The compound effectively attenuated the biofilm formation and competence development of S...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642031/clustering-of-ms-2-spectra-using-unsupervised-methods-to-aid-the-identification-of-secondary-metabolites-from-pseudomonas-aeruginosa
#7
Tobias Depke, Raimo Franke, Mark Brönstrup
Pseudomonas aeruginosa is an important opportunistic pathogen that produces a large arsenal of small molecule virulence factors and quorum sensing signal molecules. The annotation of these secondary metabolites in untargeted, mass spectrometry-based metabolomics is difficult, as many of them cannot be found in common metabolite databases, and as manual annotation is tedious. We therefore developed an algorithm named CluMSID that uses cosine similarities of product ion spectra and neutral loss patterns in combination with unsupervised clustering methods such as multidimensional scaling, density based clustering and hierarchical clustering to group structurally similar compounds and hence facilitate their annotation...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28641512/molecular-docking-and-molecular-dynamics-simulation-based-approach-to-explore-the-dual-inhibitor-against-hiv-1-reverse-transcriptase-and-integrase
#8
Subhash Chander, Rajan Kumar Pandey, Ashok Penta, Bhanwar Singh Choudhary, Manish Sharma, Ruchi Malik, Vijay Kumar Prajapati, Sankaranarayanan Murugesan
HIV integrase (IN) and reverse transcriptase (RT) are key enzymes for the replication of HIV-1. DNA polymerase and ribonuclease H (RNase H) are the two catalytic domains of HIV-1 RT which are validated as drug targets because of their essence for replication. IN and RNase H domain of RT share the striking structural similarity; it contains conserved DDE triad (two aspartates and one glutamate) and a pair of divalent Mg2+/Mn2+ ions at their catalytic core domain. Therefore, the search of compounds with dual inhibition of IN and RNase H can be the viable and more efficacious approach for the drug development against both wild and drug resistance strains of HIV...
June 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28641420/nh3-as-unique-non-classical-content-former-within-clathrate-hydrates
#9
Zafer Maşlakcı, J Paul Devlin, Nevin Uras-Aytemiz
High quality FTIR spectra of aerosols of NH3-THF and NH3-TMO binary clathrate hydrates (CHs) have been measured. Our recently developed all-vapor sub-second approach to clathrate-hydrate formation combined with computational studies has been used to identify vibrational spectroscopic signatures of NH3 within the gas hydrates. The present study shows that there are three distinct NH3 types, namely, classical small-cage NH3, nonclassical small-cage NH3, and NH3 within the hydrate network. The network ammonia does not directly trigger the non-classical CH structure...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28640596/drug-target-kinetics-in-drug-discovery
#10
Peter J Tonge
The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation...
June 22, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28639727/switching-futile-para-quinone-to-efficient-ros-generator-ubiquitin-specific-protease-2-inhibition-electrocatalysis-and-quantification
#11
Ashraf Brik, Pushparathinam Gopinath, Atif Mahammed, Tal Eilon-Shaffer, Mickal Nawatha, Shimrit Ohayon, Doron Shabat, Zeev Gross
Understanding the correlation between structural features of small molecule drugs to its mode of action is a fascinating topic and crucial for the drug discovery process. However, in many cases the exact parameters that dictate the mode of action is still lacking. Following a large screening for USP2 inhibition identified effective para-quinone based inhibitor with unclear mode of action. For gaining a deep knowledge on its mechanism of inhibition, a set of para-quinones was prepared and studied for USP2 inhibition, electrocatalysis and ROS quantification...
June 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28637405/molecular-dynamics-simulations-challenges-and-opportunities-a-biologist-s-prospective
#12
Indu Kumari, Padmani Sandhu, Mushtaq Ahmed, Yusuf Akhter
Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules...
June 21, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28637319/matrix-metalloproteinases-their-functional-role-in-lung-cancer
#13
Neha Merchant, Ganji Purnachandra Nagaraju, Balney Rajitha, Saipriya Lammata, Kishore Kumar Jella, Zachary S Buchwald, Sajani S Lakka, Arif N Ali
Lung malignancy is the foremost cause of cancer-related deaths globally and is frequently related to long-term tobacco smoking. Recent studies reveal that the expression of matrix metalloproteinases (MMPs) is extremely high in lung tumors compared to non-malignant lung tissue. MMPs are zinc-dependent proteases and are involved in the degradation of extracellular matrix (ECM). Several investigations have shown that MMPs manipulate the activity of non-ECM molecules, including cytokines, growth factors and receptors which control the tumor microenvironment...
June 16, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#14
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28636951/structure-of-cc-chemokine-receptor-5-with-a-potent-chemokine-antagonist-reveals-mechanisms-of-chemokine-recognition-and-molecular-mimicry-by-hiv
#15
Yi Zheng, Gye Won Han, Ruben Abagyan, Beili Wu, Raymond C Stevens, Vadim Cherezov, Irina Kufareva, Tracy M Handel
CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc...
June 20, 2017: Immunity
https://www.readbyqxmd.com/read/28636911/direct-conversion-of-an-enzyme-from-native-like-to-amyloid-like-aggregates-within-inclusion-bodies
#16
Francesco Elia, Francesca Cantini, Fabrizio Chiti, Christopher Martin Dobson, Francesco Bemporad
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636874/next-generation-matrix-metalloproteinase-inhibitors-novel-strategies-bring-new-prospects
#17
REVIEW
Maxim Levin, Yael Udi, Inna Solomonov, Irit Sagi
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior...
June 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28636681/thermally-induced-conformational-changes-and-protein-protein-interactions-of-bovine-serum-albumin-in-aqueous-solution-under-different-ph-and-ionic-strengths-as-revealed-by-saxs-measurements
#18
Dmitry Molodenskiy, Evgeny Shirshin, Tatiana Tikhonova, Andrey Gruzinov, Georgy Peters, Francesco Spinozzi
Thermal-induced conformational changes and protein-protein interactions of bovine serum albumin (BSA) in aqueous solution are assessed by small angle X-ray scattering (SAXS) at two pH values (7.4 and 9.0) and two ionic strengths (0.1 and 0.5). We demonstrate that Guinier analysis in two ranges of the modulus of the scattering vector allows protein melting and aggregation to be monitored simultaneously, thus providing insights into the mechanism of thermal-induced BSA aggregation. Results of the analysis suggest that at room temperature monomeric and dimeric BSA fractions are present in solution...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636330/water-in-ionic-liquid-lubricants-friend-and-foe
#19
Oscar Y Fajardo, Fernando Bresme, Alexei A Kornyshev, Michael Urbakh
To a greater or lesser extent, most room temperature ionic liquids (RTILs) absorb water from humid air. Penetration of water into the lubricating nanoscale film may affect its equilibrium structure and dynamic properties and thus influence the ability of RTILs as lubricants to reduce friction between solid surfaces. Here we investigate the impact of hydration on lubrication using non-equilibrium molecular dynamics simulations. Water adsorption changes both the ionic liquid molecules orientation and the slip conditions at the solid-liquid interfaces, resulting in a reduced resistance against squeezing-out of the lubricant by an external load...
June 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#20
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
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