X-ray crystallography-promoted drug design of carbonic anhydrase inhibitors

2015 ◽  
Vol 51 (33) ◽  
pp. 7108-7111 ◽  
Author(s):  
Jekaterina Ivanova ◽  
Janis Leitans ◽  
Muhammet Tanc ◽  
Andris Kazaks ◽  
Raivis Zalubovskis ◽  
...  
Keyword(s):  
Drug Design ◽  
Carbonic Anhydrase ◽  
Carbonic Anhydrase Inhibitors ◽  
X Ray ◽  
X Ray Crystallography ◽  
Crystallization Experiments ◽  
Hydrolysis Of

The X-ray co-crystallization experiments of saccharin derivative with carbonic anhydrase revealed hydrolysis of isothiazole ring of saccharin and guided design of new inhibitors.

X-Ray Crystallography of Carbonic Anhydrase Inhibitors and Its Importance in Drug Design

2009 ◽  
pp. 138-66 ◽  
Author(s):  
Vincenzo Alterio ◽  
Anna Di Fiore ◽  
Katia D'Ambrosio ◽  
Claudiu T. Supuran ◽  
Giuseppina De Simone
Keyword(s):  
Drug Design ◽  
Carbonic Anhydrase ◽  
Carbonic Anhydrase Inhibitors ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Hydrophobic Substituents of the Phenylmethylsulfamide Moiety Can Be Used for the Development of New Selective Carbonic Anhydrase Inhibitors

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Giuseppina De Simone ◽  
Ginta Pizika ◽  
Simona Maria Monti ◽  
Anna Di Fiore ◽  
Jekaterina Ivanova ◽  
...  
Keyword(s):  
Drug Design ◽  
Carbonic Anhydrase ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Zinc Binding ◽  
Binding Mechanism ◽  
Carbonic Anhydrase Inhibitors ◽  
X Ray ◽  
Human Carbonic Anhydrase ◽  
Hydrophobic Cleft

A new series of compounds containing a sulfamide moiety as zinc-binding group (ZBG) has been synthesized and tested for determining inhibitory properties against four human carbonic anhydrase (hCA) isoforms, namely, CAs I, II, IX, and XII. The X-ray structure of the cytosolic dominant isoform hCA II in complex with the best inhibitor of the series has also been determined providing further insights into sulfamide binding mechanism and confirming that such zinc-binding group, if opportunely derivatized, can be usefully exploited for obtaining new potent and selective CAIs. The analysis of the structure also suggests that for drug design purposes the but-2-yn-1-yloxy moiety tail emerges as a very interesting substituent of the phenylmethylsulfamide moiety due to its capability to establish strong van der Waals interactions with a hydrophobic cleft on the hCA II surface, delimited by residues Phe131, Val135, Pro202, and Leu204. Indeed, the complementarity of this tail with the cleft suggests that different substituents could be used to discriminate between isoforms having clefts with different sizes.

Preparation and structural analysis of (±)-threo-ritalinic acid

2013 ◽  
Vol 69 (11) ◽  
pp. 1225-1228 ◽  
Author(s):  
Sara Wyss ◽  
Irmgard A. Werner ◽  
W. Bernd Schweizer ◽  
Simon M. Ametamey ◽  
Selena Milicevic Sephton
Keyword(s):  
Methyl Ester ◽  
Free Acid ◽  
Nmr Analysis ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ph Values ◽  
Ritalinic Acid ◽  
Methyl Phenidate ◽  
Hydrolysis Of

Hydrolysis of the methyl ester (±)-threo-methyl phenidate afforded the free acid in 40% yield,viz.(±)-threo-ritalinic acid, C13H17NO2. Hydrolysis and subsequent crystallization were accomplished at pH values between 5 and 7 to yield colourless prisms which were analysed by X-ray crystallography. Crystals of (±)-threo-ritalinic acid belong to theP21/nspace group and form intermolecular hydrogen bonds. An antiperiplanar disposition of the H atoms of the (HOOC—)CH—CHpygroup (py is pyridine) was found in both the solid (diffraction analysis) and solution state (NMR analysis). It was also determined that (±)-threo-ritalinic acid conforms to the minimization of negativegauche+–gauche−interactions.

scholarly journals Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol

IUCrJ ◽  
2015 ◽  
Vol 2 (5) ◽  
pp. 534-544 ◽  
Author(s):  
S. Fili ◽  
A. Valmas ◽  
M. Norrman ◽  
G. Schluckebier ◽  
D. Beckers ◽  
...  
Keyword(s):  
Human Insulin ◽  
Organic Ligand ◽  
European Synchrotron Radiation Facility ◽  
X Ray Diffraction ◽  
Ph Variation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Swiss Light Source ◽  
Crystallization Experiments ◽  
Ph Range

This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.

scholarly journals Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1211-C1211
Author(s):  
Joseph Ng ◽  
Ronny Hughes ◽  
Michelle Morris ◽  
Leighton Coates ◽  
Matthew Blakeley ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Inorganic Pyrophosphatase ◽  
Inorganic Pyrophosphate ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Crystallographic Structures ◽  
Hydrolysis Of ◽  
Low Energy Conformations

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.

Catalyst-Free Synthesis of Diastereomerically Pure 3-Sulfonyl­azetidin-2-ones via Microwave-Assisted Tandem Wolff Rearrangement–Staudinger Cycloaddition

Synthesis ◽  
2020 ◽  
Author(s):  
Mikhail Krasavin ◽  
Judith Synofzik ◽  
Olga Bakulina ◽  
Olga Balabas ◽  
Dmitry Dar’in
Keyword(s):  
Drug Design ◽  
Single Crystal ◽  
Wolff Rearrangement ◽  
X Ray ◽  
Design And Optimization ◽  
X Ray Crystallography ◽  
Microwave Assisted ◽  
Catalyst Free ◽  
Relative Stereochemistry ◽  
Wide Range

A wide range of α-diazo-β-ketosulfones have been applied to thermally promoted tandem Wolff rearrangement – Staudinger [2+2] cycloaddition with imines to give polysubstituted β-lactam sulfones. Dia­stereomerically pure syn-diastereomers were obtained in good yields and the relative stereochemistry was confirmed by single-crystal X-ray crystallography. These findings significantly expand the scope of this transformation, in contrast to substantial limitations reported previously. Moreover, this methodology enables flexible exploration of new substitution patterns around the privileged β-lactam core for drug design and optimization.

scholarly journals The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design

2020 ◽  
Author(s):  
Oleg Y. Borbulevych ◽  
Roger I. Martin ◽  
Lance M. Westerhoff
Keyword(s):  
Drug Design ◽  
Critical Role ◽  
Pharmaceutical Research ◽  
Energy Functional ◽  
Structural Refinement ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
Refinement Method ◽  
The Impact

Abstract Conventional protein:ligand crystallographic refinement uses stereochemistry restraints coupled with a rudimentary energy functional to ensure the correct geometry of the model of the macromolecule—along with any bound ligand(s)—within the context of the experimental, X-ray density. These methods generally lack explicit terms for electrostatics, polarization, dispersion, hydrogen bonds, and other key interactions, and instead they use pre-determined parameters (e.g. bond lengths, angles, and torsions) to drive structural refinement. In order to address this deficiency and obtain a more complete and ultimately more accurate structure, we have developed an automated approach for macromolecular refinement based on a two layer, QM/MM (ONIOM) scheme as implemented within our DivCon Discovery Suite and "plugged in" to two mainstream crystallographic packages: PHENIX and BUSTER. This implementation is able to use one or more region layer(s), which is(are) characterized using linear-scaling, semi-empirical quantum mechanics, followed by a system layer which includes the balance of the model and which is described using a molecular mechanics functional. In this work, we applied our Phenix/DivCon refinement method—coupled with our XModeScore method for experimental tautomer/protomer state determination—to the characterization of structure sets relevant to structure-based drug design (SBDD). We then use these newly refined structures to show the impact of QM/MM X-ray refined structure on our understanding of function by exploring the influence of these improved structures on protein:ligand binding affinity prediction (and we likewise show how we use post-refinement scoring outliers to inform subsequent X-ray crystallographic efforts). Through this endeavor, we demonstrate a computational chemistry ↔ structural biology (X-ray crystallography) "feedback loop" which has utility in industrial and academic pharmaceutical research as well as other allied fields.

scholarly journals Azobenzene-based inhibitors of human carbonic anhydrase II

2015 ◽  
Vol 11 ◽  
pp. 1129-1135 ◽  
Author(s):  
Leander Simon Runtsch ◽  
David Michael Barber ◽  
Peter Mayer ◽  
Michael Groll ◽  
Dirk Trauner ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
Carbonic Anhydrase ◽  
Drug Class ◽  
Carbonic Anhydrase Ii ◽  
Carbonic Anhydrases ◽  
X Ray ◽  
X Ray Crystallography ◽  
Human Carbonic Anhydrase

Aryl sulfonamides are a widely used drug class for the inhibition of carbonic anhydrases. In the context of our program of photochromic pharmacophores we were interested in the exploration of azobenzene-containing sulfonamides to block the catalytic activity of human carbonic anhydrase II (hCAII). Herein, we report the synthesis and in vitro evaluation of a small library of nine photochromic sulfonamides towards hCAII. All molecules are azobenzene-4-sulfonamides, which are substituted by different functional groups in the 4´-position and were characterized by X-ray crystallography. We aimed to investigate the influence of electron-donating or electron-withdrawing substituents on the inhibitory constant K i. With the aid of an hCAII crystal structure bound to one of the synthesized azobenzenes, we found that the electronic structure does not strongly affect inhibition. Taken together, all compounds are strong blockers of hCAII with K i = 25–65 nM that are potentially photochromic and thus combine studies from chemical synthesis, crystallography and enzyme kinetics.

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