Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP)

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.     

Syntheses and characterizations of three-dimensional channel-like polymeric lanthanide complexes constructed by 1,2,4,5-benzenetetracarboxylic acid

The hydrothermal reaction of YbCl(3) small middle dot6H(2)O with 1,2,4,5-benzenetetracarboxylic dianhydride resulted in [[Yb((b)btec)(1/4)((d)btec)(3/6)(H(2)O)(2)](4).6H(2)O](n)() (1) (H(4)btec = 1,2,4,5-benzenetetracarboxylic acid), and the solvothermal reaction of Er(NO(3))(3) small middle dot6H(2)O or TbCl(3).6H(2)O with 1,2,4,5-benzenetetracarboxylic dianhydride in H(2)O/acetic acid gave rise to [[Er(2)((c)btec)(2/4)((e)btec)(2/4)((f)btec)(2/4)(H(2)O)(4)].4H(2)O](n)() (2) and [[Tb(H(2)btec)(2/4)((f)btec)(3/6)(H(2)O)].2H(2)O](n)() (3), respectively. Complex 1 crystallizes in monoclinic space group C2/m with a = 20.8119(5) A, b = 17.6174(1) A, c = 5.7252(2) A, beta = 92.324(1) degrees, and Z = 1. 1 possesses a three-dimensional framework consisting of eight-coordinate ytterbium centers and two kinds of channels along the c axis. Complex 2 crystallizes in triclinic space group P with a = 9.6739(5) A, b = 11.0039(5) A, c = 11.5523 A, alpha = 104.8330(10) degrees, beta = 91.0000(10) degrees, gamma = 114.2570(10) degrees, and Z = 2. 2 has a three-dimensional framework comprising both eight- and nine-coordinate erbium centers and channels along the a axis. Complex 3 crystallizes in monoclinic space group P2(1)/n with a = 10.7246(12) A, b = 7.1693(9) A, c = 17.158(2) A, beta = 97.109(2) degrees, and Z = 4. 3 shows a three-dimensional framework containing nine-coordinate terbium centers and channels along the b axis. Uncoordinated water molecules occupy the channels in the three complexes. TGA and XRPD were determined for the three complexes, and the results illustrate that the framework of 1 is retained upon removal of uncoordinated and coordinated water molecules.     

Single molecule kinetics. I. Theoretical analysis of indicators

Single molecule experiments reveal intriguing phenomenon in chemical and biological systems. Several indicators of complex dynamics, including "intensity" correlations, "event" correlations, and characteristic functions have been proposed, but extraction of information from these indicators can be difficult since these indicators only observe certain characteristics of the system. Generally, for systems that follow Poisson kinetics, all of these indicators contain similar information about the relaxation times of the system and the connections between different relaxation times, but the information is convoluted in different ways so the strength of various indicators is system specific. The paper discusses the theoretical implications and information content of various data analysis methods for single molecule experiments and demonstrates the relationships between indicators. Under certain conditions, common indicators contain all available information about systems with Poisson kinetics between degenerate states, but extraction of this information is generally not numerically feasible. The paper also discusses practical issues associated with these analyses, which motivates a numerical study based on Bayes' formula in the companion paper [J. Witkoskie and J. S. Cao, J. Chem. Phys. 121, 6373 (2004), following paper].     

Geometries and properties of bimetallic phosphido-bridged complex Cp(CO)2W(μ-PPh2)W(CO)5 and Cp(CO)3W(μ-PPh2)W(CO)5

Complete geometry optimizations were carried out by HF and DFT methods to study the molecular structure of binuclear transition-metal compounds (Cp(CO)₃W(μ-PPh₂)W(CO)₅) (I) and (Cp(CO)₂W(μ-PPh₂)W(CO)₅) (II). A comparison of the experimental data and calculated structural parameters demonstrates that the most accurate geometry parameters are predicted by the MPW1PW91/LANL2DZ among the three DFT methods. Topological properties of molecular charge distributions were analyzed with the theory of atoms in molecules. (3, −1) critical points, namely bond critical point, were found between the two tungsten atoms, and between W1 and C10 in complex II, which confirms the existence of the metal–metal bond and a semi-bridging CO between the two tungsten atoms. The result provided a theoretical guidance of detailed study on the binuclear phosphido-bridged complex containing transition metal–metal bond, which could be useful in the further study of the heterobimetallic phosphido-bridged complexes.     

Amidinoethylation—a new reaction—IV : The amidinoethylation of alcohols: a facile synthesis of 3-alkoxy-N,N'-substituted-propanamidines

The amidinoethylation of alcohols takes place by the addition of sodium alkoxides 2 (R¹ = Me, Et) to the CC double bond of a variety of N,N'-substituted-propenamidines 1 (Method A). This illustrates the activation of the CC double bond by the conjugated amidine function and provides a new class of Michael acceptors for alcohols. However, this activation is poorer than with other nucleophiles or Michael acceptors. The amidinoethylation makes available 3-alkoxy-N,N'-substituted-amidines not easily accessible by other classical methods. However, it is demonstrated that the general N,N'-substituted-amidine synthesis via the nitrilium salts can also apply to nitrile compounds having an alkoxygroup present on the molecule (method B). Since the cyanoethylation of alcohols (4) is a very fast and facile reaction the method B is the preferred strategy for the synthesis of 3-alkoxy-N,N'-substituted-propanamidines 3.     

Strategies for multi-site GLP studies

 A GLP study can be performed at more than one site. This is called a multi-site study. Although, the study is performed at different sites, it is still one study and must completely comply with the GLP principles. The fact that different activities are conducted at different sites implies that the planning, the organization and the communication are crucial for the success of the study. This means that all the staff involved should know their responsibilities and should have the knowledge and skills to realize all the phases of the study according to the GLP principles. To achieve a well managed multi-site study, several strategies for setting up such a study can be followed. This paper focuses on the responsibilities, communication, and collaboration of the personnel, which are involved in a multi-site study. Several case studies are highlighted, and we concluded that the basic communication triangle in a single-site GLP study between test facility management, study director, and the quality assurance unit should be extended to the communication among test facility and test site management, study director, principle investigator(s), and the quality assurance units at the test sites. Introduction Received: 14 August 2002 Accepted: 26 November 2002     

Capillary electrophoresis with amperometric detection of curcumin in Chinese herbal medicine pretreated by solid-phase extraction

In the present study, curcumin from Chinese herbal medicine turmeric was determined by capillary electrophoresis with amperometric detection (CE-AD) pretreated by a self-designed, simple, inexpensive solid-phase extraction (SPE) cartridge based on the material of tributyl phosphate resin. An average concentration factor of 9 with the recovery of > 80% was achieved when applied to the analysis of curcumin in extracts of tumeric. Under the optimized CE-AD conditions: a running buffer composed of 15 mM phosphate buffer at a pH 9.7, separation voltage at 16 kV, injection for 6 s at 9 kV and detection at 1.20 V, CE-AD with SPE exhibited low detection limit as 3 x 10(-8) mol/l (S/N = 3), high efficiency of 1.0 x 10(5) N, linear range of 7 x 10(-4) -3 x 10(-6) mol/l (r = 0.9986) for curcumin extracted from light petroleum. The method developed resulted in enhancement of the detection sensitivity and reduction of interference from sample matrix in complicated samples and exhibited the potential application for routine analysis, especially in food, because a relatively complete process of sample treatment and analysis was described.     

Theoretical analysis and computer simulation of fluorescence lifetime measurements. I. Kinetic regimes and experimental time scales

The configuration-controlled regime and the diffusion-controlled regime of conformation-modulated fluorescence emission are systematically studied for Markovian and non-Markovian dynamics of the reaction coordinate. A path integral simulation is used to model fluorescence quenching processes on a semiflexible chain. First-order inhomogeneous cumulant expansion in the configuration-controlled regime defines a lower bound for the survival probability, while the Wilemski-Fixman approximation in the diffusion-controlled regime defines an upper bound. Inclusion of the experimental time window of the fluorescence measurement adds another dimension to the two kinetic regimes and provides a unified perspective for theoretical analysis and experimental investigation. We derive a rigorous generalization of the Wilemski-Fixman approximation [G. Wilemski and M. Fixman, J. Chem. Phys. 60, 866 (1974)] and recover the 1/D expansion of the average lifetime derived by Weiss [G. H. Weiss, J. Chem. Phys. 80, 2880 (1984)].     

A microwave-assisted click chemistry synthesis of 1,4-disubstituted 1,2,3-triazoles via a copper(I)-catalyzed three-component reaction

A microwave-assisted three-component reaction was used to prepare a series of 1,4-disubstituted-1,2,3-triazoles from corresponding alkyl halides, sodium azide, and alkynes. This procedure eliminates the need to handle organic azides, as they are generated in situ, making this already powerful click process even more user-friendly and safe.