J. Appl. Cryst.の発刊に際して

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.

/pdf/packmol-a-package-for-building-initial-configurations-for-qsy9r74wrw.pdf

PACKMOL: a package for building initial configurations for molecular dynamics simulations.

基礎講座 電気泳動(Electrophoresis)

It is important that the medical profession plays a significant role in critically evaluating the use of diagnostic procedures and therapies as they are introduced and tested in the detection, management, or prevention of disease states. Rigorous and expert analysis of the available data documenting absolute and relative benefits and risks of those procedures and therapies can produce helpful guidelines that improve the effectiveness of care, optimize patient outcomes, and favorably affect the overall cost of care by focusing resources on the most effective strategies.

The American College of Cardiology Foundation (ACCF) and the American Heart Association (AHA) have jointly engaged in the production of such guidelines in the area of cardiovascular disease since 1980. The ACC/AHA Task Force on Practice Guidelines, whose charge is to develop, update, or revise practice guidelines for important cardiovascular diseases and procedures, directs this effort. The Task Force is pleased to have this guideline developed in conjunction with the European Society of Cardiology (ESC). Writing committees are charged with the task of performing an assessment of the evidence and acting as an independent group of authors to develop or update written recommendations for clinical practice.

Experts in the subject under consideration have been selected from all 3 organizations to examine subject-specific data and write guidelines. The process includes additional representatives from other medical practitioner and specialty groups when appropriate. Writing committees are specifically charged to perform a formal literature review, weigh the strength of evidence for or against a particular treatment or procedure, and include estimates of expected health outcomes where data exist. Patient-specific modifiers, comorbidities, and issues of patient preference that might influence the choice of particular tests or therapies are considered as well as frequency of follow-up and cost effectiveness. When available, information from studies on cost will be considered; however, review …

/pdf/acc-aha-esc-2006-guidelines-for-management-of-patients-with-5a3f1emfzy.pdf

ACC/AHA/ESC 2006 guidelines for management of patients with ventricular arrhythmias and the prevention of sudden cardiac death

The concept of metabolite profiling has been around for decades, but technical innovations are now enabling it to be carried out on a large scale with respect to the number of both metabolites measured and experiments carried out. Here we provide a detailed protocol for gas chromatography mass spectrometry (GC-MS)-based metabolite profiling that offers a good balance of sensitivity and reliability, being considerably more sensitive than NMR and more robust than liquid chromatography-linked mass spectrometry. We summarize all steps from collecting plant material and sample handling to derivatization procedures, instrumentation settings and evaluating the resultant chromatograms. We also define the contribution of GC-MS-based metabolite profiling to the fields of diagnostics, gene annotation and systems biology. Using the protocol described here facilitates routine determination of the relative levels of 300-500 analytes of polar and nonpolar extracts in approximately 400 experimental samples per week per machine.

Gas chromatography mass spectrometry–based metabolite profiling in plants

In the last few years, fluorescence resonance energy transfer (FRET) receptor sensors have contributed to the understanding of GPCR ligand binding and functional activation. FRET sensors based on muscarinic acetylcholine receptors (mAChRs) have been employed to study dual-steric ligands, allowing for the detection of different kinetics and distinguishing between partial, full, and super agonism. Herein, we report the synthesis of the two series of bitopic ligands, 12-Cn and 13-Cn, and their pharmacological investigation at the M1, M2, M4, and M5 FRET-based receptor sensors. The hybrids were prepared by merging the pharmacophoric moieties of the M1/M4-preferring orthosteric agonist Xanomeline 10 and the M1-selective positive allosteric modulator 77-LH-28-1 (1-[3-(4-butyl-1-piperidinyl)propyl]-3,4-dihydro-2(1H)-quinolinone) 11. The two pharmacophores were connected through alkylene chains of different lengths (C3, C5, C7, and C9). Analyzing the FRET responses, the tertiary amine compounds 12-C5, 12-C7, and 12-C9 evidenced a selective activation of M1 mAChRs, while the methyl tetrahydropyridinium salts 13-C5, 13-C7, and 13-C9 showed a degree of selectivity for M1 and M4 mAChRs. Moreover, whereas hybrids 12-Cn showed an almost linear response at the M1 subtype, hybrids 13-Cn evidenced a bell-shaped activation response. This different activation pattern suggests that the positive charge anchoring the compound 13-Cn to the orthosteric site ensues a degree of receptor activation depending on the linker length, which induces a graded conformational interference with the binding pocket closure. These bitopic derivatives represent novel pharmacological tools for a better understanding of ligand-receptor interactions at a molecular level.

/pdf/novel-xanomeline-containing-bitopic-ligands-of-muscarinic-d0ribhts.pdf

Novel Xanomeline-Containing Bitopic Ligands of Muscarinic Acetylcholine Receptors: Design, Synthesis and FRET Investigation

Seit Jahren begegnet uns allen Triclosan in vielen Alltagsgegenstanden, in denen es uber eine Hemmung der Fettsauresynthese antibakteriell wirksam ist; daruber hinaus sind weitere schwach inhibierende Naturstoffe aus Bakterien und Pilzen bekannt. Die Optimierung dieser Substanzen stellt einen vielversprechenden Ansatz zur Entwicklung neuer Antituberkulotika dar, wobei sowohl die Selektivitat fur die mykobakterielle Fettsauresynthese als auch die Aufnahme der Substanzen in das Mykobakterium eine grose Hurde darstellen.

Die Fettsäuresynthese als Angriffspunkt

Robert Furchgott fand bereits in den fruhen 1980er Jahren heraus, dass Endothelzellen Substanzen produzieren, die den Tonus der Gefasmuskulatur des kardiovaskularen Systems regulieren. Die Identifizierung des Peptids Endothelin-1 (ET-1) als wichtigsten Mediator des Endothelin-Systems durch Yanagisawa 1988 und kurz darauf die Aufklarung der physiologischen Rolle der Endotheline fuhrte zu dem pharmakologischen Ansatz, die selektive Blockade der Endothelinrezeptoren therapeutisch bei der Pulmonalen Arteriellen Hypertonie (PAH) auszunutzen.

Alte und neue Endothelin‐Rezeptor‐Antagonisten. PAH und viele andere Indikationen

Various different substituted N1-phenyl-6-fluoro-7-piperazinyl-4-quinolone 3-carboxylates and the diazoniumtetrafluoroborate of sparfloxacin were tested for their ability to inhibit the growth of various Mycobacterium strains of different origin. The N1-p-hydroxylphenyl substituted compound 22 and the methoxyphenyl substituted compound missing the piperazine ring 12 were identified as promising candidates for the further development of an improved treatment of tuberculosis. In addition, compound 22 and the N1-p-fluorophenyl substituted analogue 4 were found to be active against Mycobacterium avium, which is often isolated from patients suffering from AIDS.

N1‐Phenyl Substituted 4‐Quinolones of Tuberculostatic Activity.

Abstract Capillary electrophoresis was chosen as cost-effective and robust method to separate ketamine enantiomers. For the method development, first different native and modified cyclodextrins were tested. The most promising chiral selector was α-cyclodextrin. A design of experiments (DoE) was carried out, which started with the screening of relevant factors. Based on these results, the method was optimized according to the significant factors (buffer, cyclodextrin concentration, pH value, voltage, temperature) of the screening based on the response resolution and migration time of the later migrating enantiomer. The optimized conditions consisted of a background electrolyte with 275 mM TRIS, adjusted with 85% phosphoric acid to a pH of 2.50, and 50 mM α-cyclodextrin, at a temperature of 15 °C, an applied voltage of 30 kV and an injection pressure of 1.0 psi for 10 s. A fused-silica capillary with a total length of 70 cm and an effective length to the detector of 60 cm was used. The method was validated according to ICH guideline Q2 R(1). The limit of quantification was 3.51 µg mL −1 for S-ketamine and 3.98 µg mL −1 for R-ketamine. The method showed good linearity for racemic ketamine with R 2 of 0.9995 for S-ketamine and 0.9994 for R-ketamine. The lowest quantifiable content of S-ketamine found in R-ketamine was 0.45%. 

https://link.springer.com/content/pdf/10.1007/s10337-022-04229-w.pdf

Ulrike Holzgrabe

Papers

Novel Xanomeline-Containing Bitopic Ligands of Muscarinic Acetylcholine Receptors: Design, Synthesis and FRET Investigation

Die Fettsäuresynthese als Angriffspunkt

Alte und neue Endothelin‐Rezeptor‐Antagonisten. PAH und viele andere Indikationen

N1‐Phenyl Substituted 4‐Quinolones of Tuberculostatic Activity.

Method Development, Optimization, and Validation of the Separation of Ketamine Enantiomers by Capillary Electrophoresis Using Design of Experiments