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X-ray crystallography

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https://www.readbyqxmd.com/read/27911011/fragment-based-design-synthesis-and-biological-evaluation-of-1-substituted-indole-2-carboxylic-acids-as-selective-mcl-1-inhibitors
#1
Ziqian Wang, Wenjie Xu, Ting Song, Zongwei Guo, Lu Liu, Yudan Fan, Anhui Wang, Zhichao Zhang
Based on a known selective Mcl-1 inhibitor, 6-chloro-3-(3-(4-chloro-3,5-dimethylphenoxy)propyl)-1H-indole-2-carboxylic acid, we applied a fragment-based approach to obtain new molecules that extended into the p1 pocket of the BH3 groove and then exhibited binding selectivity for the Mcl-1 over the Bcl-2 protein. After we deconstructed the 1H-indole-2-carboxylic acid from the parental molecule, a benzenesulfonyl was substituted at the 1-position to adopt a geometry preferred for accessing the p1 pocket according to the binding mode of the parental molecule identified by X-ray crystallography...
December 2, 2016: Archiv der Pharmazie
https://www.readbyqxmd.com/read/27910993/synthesis-and-full-characterization-of-an-iridium-b-h-activation-intermediate-of-the-monocarba-closo-dodecaborate-anion
#2
Yunjun Shen, Yani Pan, Jiyong Liu, Tosaporn Sattasathuchana, Kim K Baldridge, Simon Duttwyler
The preparation and full characterization of an iridium complex of the monocarba-closo-dodecaborate anion is reported. It was prepared by B-H bond activation using a tosyl amide directing group. Analysis by spectroscopic methods and X-ray crystallography revealed the presence a direct B-Ir interaction. The carborane acts as a B,N chelating ligand towards the Ir(Cp*)(solvent) fragment, resulting in a monomeric complex that is inert in solution and the solid state. Treatment with N-chlorosuccinimide resulted in selective monochlorination of the B-Ir position...
December 2, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27907874/synthesis-of-copper-and-zinc-2-pyridin-2-yl-imidazo-1-2-a-pyridine-complexes-and-their-potential-anticancer-activity
#3
Jean Dam, Zeenat Ismail, Taurai Kurebwa, Nadia Gangat, Leonie Harmse, Helder M Marques, Andreas Lemmerer, Moira L Bode, Charles B de Koning
A small library of novel copper and zinc imidazo[1,2-a]pyridine complexes have been synthesized. Their structures were confirmed by X-ray diffraction crystallography and a selection of these compounds was tested against five cancer cell lines originating from breast cancer (MCF-7 and MDA-MB-231), leukemia (K562 and HL-60) and colorectal cancer (HT-29). The imidazo[1,2-a]pyridines and their zinc complexes showed poor anticancer activity, while the copper complexes were active against the cancer cell lines with IC50 values comparable to and lower than camptothecin...
November 11, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27905149/scope-limitations-of-fmoc-chemistry-spps-based-approaches-to-the-total-synthesis-of-insulin-lispro-via-ester-insulin
#4
Stephen Kent, Balamurugan Dhayalan, Kalyaneswar Mandal, Nischay Rege, Michael Weiss, Simon Eitel, Thomas Meier, Ralph Schoenleber
We have systematically explored three approaches based on Fmoc chemistry SPPS for the total chemical synthesis of the key depsipeptide intermediate for the efficient total chemical synthesis of insulin. The approaches used were: stepwise Fmoc chemistry SPPS; the 'hybrid method', in which maximally-protected peptide segments made by Fmoc chemistry SPPS are condensed in solution; and, native chemical ligation using peptide-thioester segments generated by Fmoc chemistry SPPS. A key building block in all three approaches was a Glu[Oβ(Thr)] ester-linked dipeptide equipped with a set of orthogonal protecting groups compatible with Fmoc chemistry SPPS...
November 30, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27900844/cerium-catalyzed-hydrosilylation-of-acrylates-to-give-%C3%AE-silyl-esters
#5
Aradhana Pindwal, Smita Patnaik, William C Everett, Arkady Ellern, Theresa L Windus, Aaron D Sadow
The homoleptic organocerium complex Ce{C(SiHMe2 )3 }3 (1) reacts with B(C6 F5 )3 to produce the zwitterionic bis(alkyl) hydridoborato Ce{C(SiHMe2 )3 }2 HB(C6 F5 )3 (2). NMR and IR spectroscopy and X-ray crystallography indicate that each alkyl ligand contains two bridging Ce↼H-Si interactions in both 1 and 2. Compound 2 serves as a precatalyst for the hydrosilylation of acrylates to give α-silyl esters at room temperature with a turnover number of 2200.
November 30, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27900555/x-ray-crystallography-as-a-tool-to-determine-three-dimensional-structures-of-commercial-enzymes-subjected-to-treatment-in-pressurized-fluids
#6
REVIEW
Mirian Cristina Feiten, Marco Di Luccio, Karine F Santos, Débora de Oliveira, J Vladimir Oliveira
The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity...
November 29, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27900513/synthesis-and-antimicrobial-evaluation-of-ester-linked-1-4-disubstituted-1-2-3-triazoles-with-a-furyl-thienyl-moiety
#7
C P Kaushik, Raj Luxmi, Dharmendra Singh, Ashwani Kumar
Twenty ester-linked 1,4-disubstituted 1,2,3-triazoles having a furyl/thienyl moiety have been synthesized from heteroaryl prop-2-yn-1-yl carboxylate and aromatic azides via a Cu(I) catalyzed 1,3-dipolar cycloaddition. All the synthesized compounds were characterized by FTIR, [Formula: see text]H NMR, [Formula: see text]C NMR spectroscopy and HRMS. Synthesized triazoles were tested in vitro for antimicrobial evaluation against Gram-negative bacteria-Escherichia coli, Enterobacter aerogenes and Klebsiella pneumoniae; Gram-positive bacteria-Staphylococcus aureus and two fungal strains-Candida albicans and Aspergillus niger, reflecting moderate to good activity...
November 29, 2016: Molecular Diversity
https://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#8
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897427/structure-based-drug-design-of-mineralocorticoid-receptor-antagonists-to-explore-oxosteroid-receptor-selectivity
#9
Anneli Nordqvist, Gavin O'Mahony, Maria Fridén-Saxin, Marlene Fredenwall, Anders Hogner, Kenneth L Granberg, Anna Aagaard, Stefan Bäckström, Anders Gunnarsson, Tim Kaminski, Yafeng Xue, Anita Dellsén, Eva Hansson, Pia Hansson, Ida Ivarsson, Ulla Karlsson, Krister Bamberg, Majlis Hermansson, Jennie Georgsson, Bo Lindmark, Karl Edman
The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of non-steroidal MR antagonists to improve selectivity over other members of the oxosteroid receptor family. A biaryl sulfonamide compound was identified in a high-throughput screening (HTS) campaign. The compound bound to MR with a pKi=6.6, but displayed poor selectivity over the glucocorticoid receptor (GR) and the progesterone receptor (PR)...
November 29, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27897281/platinum-ii-o-s-complexes-as-potential-metallodrugs-against-cisplatin-resistance
#10
Jana Hildebrandt, Norman Häfner, Helmar Görls, Daniel Kritsch, Giarita Ferraro, Matthias Dürst, Ingo B Runnebaum, Antonello Merlino, Wolfgang Weigand
We report on platinum(ii) complexes with different cinnamic acid derivatives as ligands with cytotoxic activity against Cisplatin resistant ovarian cancer cell line subcultures of SKOV3 and A2780. A typical mechanism of action for platinum(ii) complexes as Cisplatin itself is binding to the DNA and inducing double-strand breaks. We examined the biological behavior of these potential drugs with 9-methylguanine using NMR spectroscopic methods and their DNA damage potential including γH2AX-foci analyses. X-ray diffraction methods have been used to elucidate the molecular structures of the platinum(ii) complexes...
November 29, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27896733/3d-computational-modeling-of-proteins-using-sparse-paramagnetic-nmr-data
#11
Kala Bharath Pilla, Gottfried Otting, Thomas Huber
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896717/a-practical-approach-to-protein-crystallography
#12
Andrea Ilari, Carmelinda Savino
Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895259/arene-guest-selectivity-and-pore-flexibility-in-a-metal-organic-framework-with-semi-fluorinated-channel-walls
#13
Rebecca Smith, Iñigo J Vitórica-Yrezábal, Adrian Hill, Lee Brammer
A metal-organic framework (MOF) with one-dimensional channels of approximately hexagonal cross-section [Ag2(O2CCF2CF2CO2)(TMP)] 1: (TMP =2,3,5,6-tetramethylpyrazine) has been synthesized with MeOH filling the channels in its as-synthesized form as [Ag2(O2CCF2CF2CO2)(TMP)]·n(MeOH) 1-MEOH: (n = 1.625 by X-ray crystallography). The two types of ligand connect columns of Ag(I) centres in an alternating manner, both around the channels and along their length, leading to an alternating arrangement of hydrocarbon (C-H) and fluorocarbon (C-F) groups lining the channel walls, with the former groups projecting further into the channel than the latter...
January 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/27895258/x-ray-crystallographic-insights-into-post-synthetic-metalation-products-in-a-metal-organic-framework
#14
Michael T Huxley, Campbell J Coghlan, Witold M Bloch, Alexandre Burgun, Christian J Doonan, Christopher J Sumby
Post-synthetic modification of metal-organic frameworks (MOFs) facilitates a strategic transformation of potentially inert frameworks into functionalized materials, tailoring them for specific applications. In particular, the post-synthetic incorporation of transition-metal complexes within MOFs, a process known as 'metalation', is a particularly promising avenue towards functionalizing MOFs. Herein, we describe the post-synthetic metalation of a microporous MOF with various transition-metal nitrates. The parent framework, 1: , contains free-nitrogen donor chelation sites, which readily coordinate metal complexes in a single-crystal to single-crystal transformation which, remarkably, can be readily monitored by X-ray crystallography...
January 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/27894775/synthesis-characterization-and-biological-studies-of-schiff-bases-derived-from-heterocyclic-moiety
#15
Angamaly Antony Shanty, Jessica Elizabeth Philip, Eeettinilkunnathil Jose Sneha, Maliyeckal R Prathapachandra Kurup, Sreedharannair Balachandran, Puzhavoorparambil Velayudhan Mohanan
Some new Schiff bases (H1-H7) have been synthesized by the condensation of 2-aminophenol, 2-amino-4-nitrophenol, 2-amino-4-methylphenol, 2-amino benzimidazole with thiophene-2-carboxaldehyde and pyrrole-2-carboxaldehyde. The structures of newly synthesized compounds were characterized by elemental analysis, FT-IR, (1)H NMR, UV-VIS, and single crystal X-ray crystallography. The in vitro antibacterial activity of the synthesized compounds has been tested against Salmonella typhi, Bacillus coagulans, Bacillus pumills, Escherichia coli, Bacillus circulans, Pseudomonas, Clostridium and Klebsilla pneumonia by disk diffusion method...
November 21, 2016: Bioorganic Chemistry
https://www.readbyqxmd.com/read/27891613/a-review-of-spectroscopic-and-biophysical-chemical-studies-of-the-complex-of-cpd-photolyase-and-cryptochrome-dash-with-substrate-dna
#16
Johannes P M Schelvis, Yvonne M Gindt
CPD photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair cyclobutane pyrimidine dimers (CPD) on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, though some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue-light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH...
November 28, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27891541/dft-calculations-in-the-assignment-of-solid-state-nmr-and-crystal-structure-elucidation-of-a-lanthanum-iii-complex-with-dithiocarbamate-and-phenanthroline
#17
Vasantha Gowda, Risto S Laitinen, Ville-Veikko Telkki, Anna-Carin Larsson, Oleg N Antzutkin, Perttu Lantto
The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state (13)C and (15)N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and (13)C and (15)N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P21/n...
November 28, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27889471/functional-characterization-of-two-naturally-occurring-mutations-v-221-g-and-t-449-n-in-the-follicle-stimulating-hormone-receptor
#18
Antara A Banerjee, Swati K Achrekar, Shaini Joseph, Bhakti R Pathak, Smita D Mahale
Naturally occurring mutations in follicle stimulating hormone receptor (FSHR) affect the receptor function. Here, we characterized two such previously reported mutations, V(221)G and T(449)N, in the extracellular domain and transmembrane helix 3, of FSHR, respectively. Functional studies with the V(221)G mutant demonstrated an impairment in FSH binding and signaling. Validation of X-ray crystallography data indicating the contribution of FSHR specific residues in the vicinity of V(221) to contribute to FSH-FSHR interaction was carried out...
November 23, 2016: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/27889071/using-x-ray-crystallography-to-simplify-and-accelerate-biologics-drug-development
#19
REVIEW
Mark L Brader, Edward N Baker, Michael F Dunn, Thomas M Laue, John F Carpenter
Every major biopharmaceutical company incorporates a protein crystallography unit that is central to its structure-based drug discovery efforts. Yet these capabilities are rarely leveraged toward the formal higher order structural characterization that is so challenging but integral to large-scale biologics manufacturing. Although the biotech industry laments the shortcomings of its favored biophysical techniques, x-ray crystallography is not even considered for drug development. Why not? We suggest that this is due, at least in part, to outdated thinking (for a recent industry-wide survey, see Gabrielson JP, Weiss IV WF...
November 23, 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27886433/the-burkholderia-cenocepacia-peptidoglycan-associated-lipoprotein-is-involved-in-epithelial-cell-attachment-and-elicitation-of-inflammation
#20
Ruth Dennehy, Maria Romano, Alessia Ruggiero, Yasmine F Mohamed, Simon L Dignam, Cristóbal Mujica Troncoso, Máire Callaghan, Miguel A Valvano, Rita Berisio, Siobhán McClean
The Burkholderia cepacia complex (Bcc) is a group of Gram-negative opportunistic pathogens causing infections in people with cystic fibrosis (CF). Bcc is highly antibiotic resistant, making conventional antibiotic treatment problematic. The identification of novel targets for anti-virulence therapies should improve therapeutic options for infected CF patients. We previously identified that the peptidoglycan-associated lipoprotein (Pal) was immunogenic in Bcc infected CF patients; however, its role in Bcc pathogenesis is unknown...
November 7, 2016: Cellular Microbiology
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