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Small molecule structure

Morteza Chehelamirani, Maurício C da Silva, Dennis R Salahub
Electronic properties of carbon nanotubes (CNTs) play an important role in their interactions with nano-structured materials. In this work, interactions of adenosine monophosphate (AMP), a DNA nucleotide, with metallic and semi-conducting CNTs are studied using the density functional tight binding (DFTB) method. The electronic structure of semi-conducting CNTs was found to be changed as they turned to metallic CNTs in a vacuum upon interaction with the nucleotide while metallic CNTs remain metallic. Specifically, the band gap of semi-conducting CNTs was decreased by 0...
February 27, 2017: Physical Chemistry Chemical Physics: PCCP
Ashley M Smith, Jill E Millstone
The use of nanoparticles in biomedicine critically depends on their surface chemistry. For metal nanoparticles, a common way to tune this surface chemistry is through mass action ligand exchange, where ligand exchange can be used to expand the functionality of the resulting nanoparticle conjugates. Specifically, the quantity, identity, and arrangement of the molecules in the resulting ligand shell each can be tuned significantly. Here, we describe methods to exchange and quantify thiolated and non-thiolated ligands on gold nanoparticle surfaces...
2017: Methods in Molecular Biology
Harikrishna Reddy R, Hackyoung Kim, Seungbin Cha, Bongsoo Lee, Young Jun Kim
Phosphorylation is a critical mechanism in biological systems and it is estimated that phosphorylation is indispensable for about 30% of key biological activities such as cell cycle progression, migration, and division. It is synergistically balanced by kinases and phosphatases, and any deviation from this balance leads to diseased conditions. Pathway or biological activity based abnormalities in phosphorylation and the type of involved phosphatase influence the outcome and cause diverse diseases ranging from diabetes, rheumatoid arthritis, and numerous cancers...
February 24, 2017: Journal of Microbiology and Biotechnology
Shaoying Wang, Zhi Zhou, Zhengyi Zhao, Hui Zhang, Farzin Haque, Peixuan Guo
Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the passage of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures...
January 30, 2017: Biomaterials
Yahui Pan, Wenzhe Pang, Jie Lv, Jing Wang, Caiqin Yang, Wei Guo
In present study, based on the two polymorphs (α and β form) of azelnidipine (AZE), 12 complexes of AZE and oxalic acid (OXA) were prepared by solvent-assisted grinding (SG) and neat powder grinding (NG) methods at the AZE/OXA molar ratios of 2:1, 1:1, and 1:2. The effect of the different polymorphs of AZE on the micro-structure of the complexes were investigated by powder X-ray diffraction (PXRD), tempreture modulated differential scanning calorimetry and thermogravimetric analysis, cryo-field emission scanning electron microscope system, fourier transform infrared (FTIR), and solid-state nuclear magnetic resonance spectroscopy...
February 4, 2017: Journal of Pharmaceutical and Biomedical Analysis
Jiawen Chen, Yinghao Wu
Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs) which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so many extracellular domains need to be evolved through natural selection. We tackled this problem by computational modeling. A generic model of CAMs was constructed based on domain organization of neuronal cell adhesion molecule (NrCAM), which is engaged in maintaining neuron-neuron adhesion in central nervous system...
February 22, 2017: Journal of Molecular Biology
Oliviero Carugo
The positions of water molecules have been analyzed in high quality protein X-ray crystal structures. About 70% of these water molecules are in contact with protein atoms at the protein surface and constitute the first hydration layer. About 20% of them are close to the first hydration layer but are not in contact with protein atoms and constitute the second hydration layer. The rest of the water molecules are either buried in the protein core or close to hetero-atoms (inorganic ions and small organic molecules)...
February 22, 2017: International Journal of Biological Macromolecules
Sean Ekins, Adwait Anand Godbole, György Kéri, Lászlo Orfi, János Pato, Rajeshwari Subray Bhat, Rinkee Verma, Erin K Bradley, Valakunja Nagaraja
There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target in this regard. However, it suffers from a shortage of known inhibitors. We have previously used computational approaches such as homology modeling and docking to propose 38 FDA approved drugs for testing and identified several active molecules. To follow on from this, we now describe the in vitro testing of a library of 639 compounds...
March 2017: Tuberculosis
P Maturana, M Martinez, M E Noguera, N C Santos, E A Disalvo, L Semorile, P C Maffia, A Hollmann
Antimicrobial peptides (AMPs) are small cationic molecules that display antimicrobial activity against a wide range of bacteria, fungi and viruses. For an AMP to be considered as a therapeutic option, it must have not only potent antibacterial properties but also low hemolytic and cytotoxic activities [1]. Even though many studies have been conducted in order to correlate the antimicrobial activity with affinity toward model lipid membranes, the use of these membranes to explain cytotoxic effects (especially hemolysis) has been less explored...
February 13, 2017: Colloids and Surfaces. B, Biointerfaces
Mahzad Sharifahmadian, Tarun Arya, Benoit Bessette, Lauriane Lecoq, Edward Ruediger, James G Omichinski, Christian Baron
Secretion systems are protein complexes essential for bacterial virulence and potential targets for anti-virulence drugs. In the intracellular pathogen Brucella suis, a type IV secretion system mediates the translocation of virulence factors into host cells and it is essential for pathogenicity. VirB8 is a core component of the secretion system and dimerization is important for functionality of the protein complex. We set out to study dimerization and possible conformational changes of VirB8 from Brucella suis (VirB8s) using nuclear magnetic resonance, X-ray crystallography and differential scanning fluorimetry...
February 25, 2017: FEBS Journal
Hewen Zheng, Nischal Singh, Gauri S Shetye, Yucheng Jin, Diana Li, Yan-Yeung Luk
Rhamnolipids secreted by Pseudomonas aeruginosa are required for the bacteria to form biofilm efficiently and form biofilm with internal structures including pores and channels. In this work, we explore the effect of a class of synthetic analogs of rhamnolipids at controlling (promoting and inhibiting) the biofilm formation activities of a non-rhamnolipid-producing strain - rhlA - of P. aeruginosa. This class of rhamnolipid analogs is known to modulate the swarming motilities of wild-type PAO1 and rhlA mutant, but its effect on biofilm formation of rhlA mutant is unknown...
February 1, 2017: Bioorganic & Medicinal Chemistry
Timothy R Siegert, Michael Bird, Joshua A Kritzer
Peptides are an increasingly useful class of molecules, finding unique applications as chemical probes and potential drugs. They are particularly adept at inhibiting protein-protein interactions, which are often difficult to target using small molecules. The identification and rational design of protein-binding epitopes remains a bottleneck in the development of bioactive peptides. One fruitful strategy has been using structured scaffolds to present essential hot spot residues involved in protein-protein recognition, and this process has been greatly advanced by computational tools that can identify hot spot residues...
2017: Methods in Molecular Biology
Imanol Usabiaga, Jorge González, Iker León, Pedro F Arnaiz, Emilio J Cocinero, José A Fernández
Carbohydrates are, together with amino acids, DNA bases, and lipids, the building blocks of living beings. They play a central role in basic functions such as immunity and signaling, which are governed by noncovalent interactions between sugar units and other biomolecules. To get insights into such interactions between monosaccharide units, we used a combination of mass-resolved laser spectroscopy in supersonic expansions and molecular structure calculations. The results obtained clearly demonstrate that the small stability difference between the α/β anomers of glucopyranose derivatives is reversed and amplified during molecular aggregation, making the complexes of the β-anomers significantly more stable...
February 24, 2017: Journal of Physical Chemistry Letters
Carlos A Sanhueza, Michael M Baksh, Benjamin Thuma, Marc D Roy, Sanjay Dutta, Cathy Préville, Boris A Chrunyk, Kevin Beaumont, Robert Dullea, Mark Ammirati, Shenping Liu, David Gebhard, James E Finley, Christopher T Salatto, Amanda King-Ahmad, Ingrid Stock, Karen Atkinson, Benjamin Reidich, Wen Lin, Rajesh Kumar, Meihua Tu, Elnaz Menhaji-Klotz, David A Price, Spiros Liras, M G Finn, Vincent Mascitti
A compact and stable bicyclic bridged ketal was developed as a ligand for the asialoglycoprotein receptor (ASGPR). This compound showed excellent ligand efficiency, and the molecular details of binding were revealed by the first X-ray crystal structures of ligand-bound ASGPR. This analogue was used to make potent di- and trivalent binders of ASGPR. Extensive characterization of the function of these compounds showed rapid ASGPR-dependent cellular uptake in vitro and high levels of liver/plasma selectivity in vivo...
February 23, 2017: Journal of the American Chemical Society
Sergey N Filimonov, Wei Liu, Alexandre Tkatchenko
The design of novel elementary surface processes is important for applications in catalysis, single-molecule junctions, molecular sensors, switches and surface mounted molecular machines. Here we demonstrate by van der Waals inclusive density functional theory calculations that a small and relatively simple heteroaromatic compound s-triazine (C$_3$H$_3$N$_3$) unexpectedly possesses five metastable states when adsorbed on the Pt(111) surface. This diversity of the adsorption states stems from an interplay between versatile molecule/surface chemical bonding and van der Waals interactions and from ``softening'' of the aromatic ring by nitrogen substitution, which makes folding of the aromatic ring energetically much less demanding as compared to benzene...
February 23, 2017: Journal of Physical Chemistry Letters
Lei Wu, Shu-Hou Yang, Hao Xiong, Jia-Qian Yang, Jun Guo, Wen-Chao Yang, Guang-Fu Yang
We report herein a non-peptide-based small molecule probe for fluorogenic and chromogenic detection of chymotrypsin, and the primary application. This probe was rationally designed by mimicking the peptide substrate and optimized by adjusting the recognization group. The refined probe 2 exhibits good specificity toward chymotrypsin, producing about 25-fold higher enhancement in both the fluorescence intensity and absorbance upon the catalysis by chymotrypsin. Compared with the most widely used peptide substrate (AMC-FPAA-Suc) of chymotrypsin, probe 2 shows about 5-fold higher binding affinity, and comparable catalytical efficiency against chymotrypsin...
February 23, 2017: Analytical Chemistry
Markus Rauhalahti, Stefan Taubert, Dage Sundholm, Vincent Liégeois
Magnetically induced current density susceptibilities and ring-current strengths have been calculated for neutral and doubly charged persubstituted benzenes C6X6 and C6X6(2+) with X = F, Cl, Br, I, At, SeH, SeMe, TeH, TeMe, and SbH2. The current densities have been calculated using the gauge-including magnetically induced current (GIMIC) method, which has been interfaced to the Gaussian electronic structure code rendering current density calculations using effective core potentials (ECP) feasible. Relativistic effects on the ring-current strengths have been assessed by employing ECP calculations of the current densities...
February 23, 2017: Physical Chemistry Chemical Physics: PCCP
Wangkhem P Singh, Rajkumar S Singh
In the present work, we have explored the use of the triphenylmethyl group, a commonly used protecting group for primary alcohols as a gelling structural component in the design of molecular gelators. We synthesized a small library of triphenylmethyl derivatives of simple primary alcohols and studied their gelation properties in different solvents. Gelation efficiency for some of the derivatives was moderate to excellent with a minimum gelation concentration ranging between 0.5-4.0% w/v and a gel-sol transition temperature range of 31-75 °C...
2017: Beilstein Journal of Organic Chemistry
Naeem Shaikh, Mahesh Sharma, Prabha Garg
Membrane transporters play a crucial role in determining fate of administered drugs in a biological system. Early identification of plausible transporters for a drug molecule can provide insights into its therapeutic, pharmacokinetic and toxicological profile. In the present study, predictive models for classifying small molecules into substrates and non-substrates of various pharmaceutically important membrane transporters are developed using QSAR and proteochemometric (PCM) approaches. For this purpose, 4575 substrate interactions for these transporters were collected from Metabolism and Transport Database (Metrabase) and literature...
February 23, 2017: Journal of Chemical Information and Modeling
Youjeong Yang, Donghoon Shin, Seunghyun Choi, Yesol Woo, Jong-Won Lee, Dongseon Kim, Hee-Young Shin, Minjun Cha, Ji-Ho Yoon
The crystal structure and guest inclusion behaviors of nitrous oxide-nitrogen (N2O-N2) binary gas hydrates formed from N2O/N2 gas mixtures are determined through spectroscopic analysis. Powder X-ray diffraction results indicate that the crystal structure of all the N2O-N2 binary gas hydrates is identified as the structure I (sI) hydrate. Raman spectra for N2O-N2 binary gas hydrate formed from N2O/N2 (80/20, 60/40, 40/60 mol %) gas mixtures reveal that N2O molecules occupy both large and small cages of the sI hydrate...
February 22, 2017: Environmental Science & Technology
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