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Small molecule structure

Matthaeus Schwarz-Schilling, Aurore Dupin, Fabio Chizzolini, Swati Krishnan, Sheref Mansy, Friedrich C Simmel
Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins - streptavidin and two fluorescent proteins - while one binds the small molecule dye malachite green (MG)...
March 22, 2018: Nano Letters
Tom Dyer, Ngamta Thamwattana, Barry Cox
The low bending rigidity of graphene facilitates the formation of folds into the structure. This curvature change affects the reactivity and electron transport of the sheet. One novel extension of this is the intercalation of small molecules into these folds. We construct a model incorporating a single-walled carbon nanotube into a sheet of folded graphene. Variational calculus techniques are employed to determine the minimum energy structure and the resulting curves are shown to agree well with molecular dynamics study...
March 22, 2018: Journal of Molecular Modeling
Lei Zhao, Jiangtao Cheng
Besides the Wenzel state, liquid droplets on micro/nanostructured surfaces can stay in the Cassie state and consequently exhibit intriguing characteristics such as a large contact angle, small contact angle hysteresis and exceptional mobility. Here we report molecular dynamics (MD) simulations of the wetting dynamics of Cassie-state water droplets on nanostructured ultrahydrophobic surfaces with an emphasis on the genesis of the contact line friction (CLF). From an ab initio perspective, CLF can be ascribed to the collective effect of solid-liquid retarding and viscous damping...
March 22, 2018: Nanoscale
Ensaf M Al-Hujaily, Tanvir Khatlani, Zeyad Alehaideb, Rizwan Ali, Bader Almuzaini, Bahauddeen M Alrfaei, Jahangir Iqbal, Imadul Islam, Shuja Malik, Bader A Marwani, Salam Massadeh, Atef Nehdi, Barrak Alsomaie, Bader Debasi, Ibraheem Bushnak, Saeed Noibi, Syed Hussain, Wahid Abdul Wajid, Jean-Pierre Armand, Sheraz Gul, Julen Oyarzabal, Rana Rais, Chas Bountra, Ahmed Alaskar, Bander Al Knawy, Mohamed Boudjelal
The 'Therapeutics discovery: From bench to first in-human trials' conference, held at the King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGHA), Kingdom of Saudi Arabia (KSA) from October 10-12, 2017, provided a unique opportunity for experts worldwide to discuss advances in drug discovery and development, focusing on phase I clinical trials. It was the first event of its kind to be hosted at the new research center, which was constructed to boost drug discovery and development in the KSA in collaboration with institutions, such as the Academic Drug Discovery Consortium in the United States of America (USA), Structural Genomics Consortium of the University of Oxford in the United Kingdom (UK), and Institute of Materia Medica of the Chinese Academy of Medical Sciences in China...
March 2018: Biomedical Reports
Guillermo Senisterra, Hugh Y Zhu, Xiao Luo, Hailong Zhang, Guoliang Xun, Chunliang Lu, Wen Xiao, Taraneh Hajian, Peter Loppnau, Irene Chau, Fengling Li, Abdellah Allali-Hassani, Peter Atadja, Counde Oyang, En Li, Peter J Brown, Cheryl H Arrowsmith, Kehao Zhao, Zhengtian Yu, Masoud Vedadi
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a multidomain protein that plays a critical role in maintaining DNA methylation patterns through concurrent recognition of hemimethylated DNA and histone marks by various domains, and recruitment of DNA methyltransferase 1 (DNMT1). UHRF1 is overexpressed in various cancers, including breast cancer. The tandem tudor domain (TTD) of UHRF1 specifically and tightly binds to histone H3 di- or trimethylated at lysine 9 (H3K9me2 or H3K9me3, respectively), and this binding is essential for UHRF1 function...
March 1, 2018: SLAS Discovery
Yoshihiro Morita, Macall Leslie, Hiroyasu Kameyama, David E Volk, Takemi Tanaka
Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small-approximately one-tenth that of monoclonal antibodies-their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules...
March 19, 2018: Cancers
Yongao Xiong, Qiongyu Li, Muchena J Kailemia, Carlito B Lebrilla, Somen Nandi, Karen A McDonald
Kifunensine, a potent and selective inhibitor of class I α-mannosidases, prevents α-mannosidases I from trimming mannose residues on glycoproteins, thus resulting in oligomannose-type glycans. We report for the first time that through one-time vacuum infiltration of kifunensine in plant tissue, N-linked glycosylation of a recombinant protein transiently produced in whole-plants shifted completely from complex-type to oligomannose-type. Fc-fused capillary morphogenesis protein 2 (CMG2-Fc) containing one N -glycosylation site on the Fc domain, produced in Nicotiana benthamiana whole plants, served as a model protein...
March 17, 2018: International Journal of Molecular Sciences
Liang Ouyang, Lan Zhang, Shouyue Zhang, Dahong Yao, Yuqian Zhao, Guan Wang, Leilei Fu, Peng Lei, Bo Liu
UNC-51-like kinase 1 (ULK1), the yeast Atg1 ortholog, is the sole serine-threonine kinase and initiating enzyme in autophagy, which may be regarded as a target in Parkinson's disease (PD). Herein, we discovered a small molecule 33i (BL-918) as a potent activator of ULK1 by structure-based drug design. Subsequently, some key amino acid residues (Arg18, Lys50, Asn86 and Tyr89) were found to be crucial to the binding pocket between ULK1 and 33i by site-directed mutagenesis. Moreover, we found that 33i induced autophagy via the ULK complex in SH-SY5Y cells...
March 21, 2018: Journal of Medicinal Chemistry
Makoto Ubukata
In this review article, I will outline my way of thinking about biologically active small molecules. The structure of liposidomycin B from Streptomyces species resulted in my initial sense that a structure tells its function. A biologically active small molecule may save directly or indirectly a number of people. Even if the molecule has not been used as a therapeutic agent, it can be used as a useful chemical probe for dissecting a living cell into different biochemical pieces. Such biologically active small molecules derived from microorganisms have been primarily found in cultivable microorganisms that make up only 1% of total microbes in nature...
March 21, 2018: Bioscience, Biotechnology, and Biochemistry
Lilong Zhang, Keli Chen, Liang He, Lincai Peng
Background: Pyrolysis has attracted growing interest as a versatile means to convert biomass into valuable products. Wheat straw has been considered to be a promising biomass resource due to its low price and easy availability. However, most of the products obtained from wheat straw pyrolysis are usually of low quality. Hot soda extraction has the advantage of selective dissolution of lignin whilst retaining the carbohydrates. This can selectively convert biomass into high-quality desired products and suppress the formation of undesirable products...
2018: Biotechnology for Biofuels
Laura Pérez-Benito, Henrik Keränen, Herman van Vlijmen, Gary Tresadern
A congeneric series of 21 phosphodiesterase 2 (PDE2) inhibitors are reported. Crystal structures show how the molecules can occupy a 'top-pocket' of the active site. Molecules with small substituents do not enter the pocket, a critical leucine (Leu770) is closed and water molecules are present. Large substituents enter the pocket, opening the Leu770 conformation and displacing the waters. We also report an X-ray structure revealing a new conformation of the PDE2 active site domain. The relative binding affinities of these compounds were studied with free energy perturbation (FEP) methods and it represents an attractive real-world test case...
March 20, 2018: Scientific Reports
Andrew J Clulow, Malinda Salim, Adrian Hawley, Elliot P Gilbert, Ben Boyd
Efforts to develop orally-administered drugs tend to place an exceptional focus on aqueous solubility as this is an essential criterion for their absorption in the gastro-intestinal tract. In this work we examine the solid state behaviour and solubility of OZ439, a promising single-dose cure for malaria being developed as the highly water-soluble mesylate salt. The aqueous phase behaviour of the OZ439 mesylate salt was determined using a combination of small angle neutron and X-ray scattering (SANS and SAXS, respectively)...
March 20, 2018: Molecular Pharmaceutics
Simon Drescher, Christian Otto, Sindy Müller, Vasil M Garamus, Christopher J Garvey, Susanne Grünert, Anke Lischka, Annette Meister, Alfred Blume, Bodo Dobner
In the present work, we describe the synthesis and the temperature-dependent aggregation behavior of a new class of asymmetrical glycerol diether bolalipid. These bolalipids are composed of a membrane-spanning alkyl chain with 32 carbon atoms (C32) in the sn-3 position, a methyl-branched C16 alkyl chain in the sn-2 position, and a zwitterionic phosphocholine headgroup in the sn-1 position of a glycerol moiety. The long C32 alkyl chain is terminated either by a second phos-phocholine (PC-Gly(2C16Me)C32-PC) or by a phosphodimethylethanolamine headgroup (PC-Gly(2C16Me)C32-Me2PE)...
March 20, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Guangye Zhang, Jingbo Zhao, Philip C Y Chow, Kui Jiang, Jianquan Zhang, Zonglong Zhu, Jie Zhang, Fei Huang, He Yan
The bulk-heterojunction blend of an electron donor and an electron acceptor material is the key component in a solution-processed organic photovoltaic device. In the past decades, a p-type conjugated polymer and an n-type fullerene derivative have been the most commonly used electron donor and electron acceptor, respectively. While most advances of the device performance come from the design of new polymer donors, fullerene derivatives have almost been exclusively used as electron acceptors in organic photovoltaics...
March 20, 2018: Chemical Reviews
Yoshito Tobe
Three isomers of quinodimethanes (QDMs) adopt different electronic configurations and geometries, generating their own characteristic physical properties. Incorporation of QDMs into non-benzenoid aromatic or antiaromatic frameworks not only planarizes the whole π system optimizing conjugation, but also changes the electronic properties inherent to QDMs, sometimes drastically, due to the topology of the π system, through interaction with the remaining part of the molecules. In non-benzenoid systems, molecular orbital levels and orbital distribution are uneven compared to benzenoid systems, thereby polarizing the ground state and leading to unique behavior in excited states...
March 20, 2018: Topics in Current Chemistry (Journal)
Jonathan Martens, Giel Berden, Herman Bentlage, Karlien L M Coene, Udo F Engelke, David Wishart, Monique van Scherpenzeel, Leo A J Kluijtmans, Ron A Wevers, Jos Oomens
The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging...
March 19, 2018: Journal of Inherited Metabolic Disease
Mathilde Koch, Amir Pandi, Baudoin Delépine, Jean-Loup Faulon
The aim of this dataset is to identify and collect compounds that are known for being detectable by a living cell, through the action of a genetically encoded biosensor and is centred on bacterial transcription factors. Such a dataset should open the possibility to consider a wide range of applications in synthetic biology. The reader will find in this dataset the name of the compounds, their InChI (molecular structure), the publication where the detection was reported, the organism in which this was detected or engineered, the type of detection and experiment that was performed as well as the name of the biosensor...
April 2018: Data in Brief
Xiaowei Dong
The blood-brain barrier (BBB) has been a great hurdle for brain drug delivery. The BBB in healthy brain is a diffusion barrier essential for protecting normal brain function by impeding most compounds from transiting from the blood to the brain; only small molecules can cross the BBB. Under certain pathological conditions of diseases such as stroke, diabetes, seizures, multiple sclerosis, Parkinson's disease and Alzheimer disease, the BBB is disrupted. The objective of this review is to provide a broad overview on current strategies for brain drug delivery and related subjects from the past five years...
2018: Theranostics
Mohamed Salla, Rodrigo Aguayo-Ortiz, Danmaliki Gaddafi Ibrahim, Alaa Zare, Ahmed Said, Jack Moore, Vrajeshkumar Pandya, Robin Manaloor, Sunny Fong, Anna R Blankstein, Spencer Gibson, Laura Ramos Garcia, Pascal Meier, Khushwant S Bhullar, Basil P Hubbard, Yahya Fiteh, Harissios Vliagoftis, Ing Swie Goping, Dion Brocks, Peter Hwang, Jose Carlos A Martinez Velazquez, Shairaz Baksh
Receptor interacting protein kinase 2 (RIP2 or RICK herein referred to as RIPK2) is linked to the pathogen pathway that activates NFkB and autophagic activation. Using molecular modeling (docking) and chemoinformatics analyses we utilized the RIPK2/ponatinib crystal structure and searched in chemical databases for small molecules exerting binding interactions similar to those exerted by ponatinib. The identified RIPK2 inhibitors potently inhibited the proliferation of cancer cells by > 70% as well as inhibition of NFkB activity...
March 19, 2018: Journal of Pharmacology and Experimental Therapeutics
Daniel Mattle, Bernd Kuhn, Johannes Aebi, Marc Bedoucha, Demet Kekilli, Nathalie Grozinger, Andre Alker, Markus G Rudolph, Georg Schmid, Gebhard F X Schertler, Michael Hennig, Jörg Standfuss, Roger J P Dawson
In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
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