Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Vibrational spectra of 2-biphenylmethanol. Spectrum simulation and molecular structure

The vibrational spectra of a solid crystalline sample of 2-biphenylmethanol have been measured at room temperature. The IR absorption spectra were recorded in the range 400 cm^–1–3600 cm^–1; Raman spectra were measured in the range 10 cm^–1–1640 cm^–1. The direct mechanical and optoelectronic problems were solved using the fragment method realized as Lev-100 software; the intensity distribution in the IR spectrum of 2-biphenylmethanol was obtained by the same method. The experimental Raman and IR absorption spectra were interpreted by analyzing the calculated data on the frequencies and forms of normal vibrations and their intensities in the IR spectra. IR absorption spectra were simulated for several models of 2-biphenylmethanol conformers that differ in the mutual orientation of fragments. Based on the results of simulation and comparison of the calculated and experimental spectra of conformers we suggested a model for the conformer realized in the solid phase under normal conditions.Original Russian Text Copyright © 2004 by L. M. Babkov, J. Baran, N. A. Davydova, J. I. Kukielskii, and S. V. TrukhachevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 624–631, July–August, 2004.This revised version was published online in April 2005 with a corrected cover date.     

Mechanism for the inhibition of the acid degradation of ampicillin by 2-hydroxypropyl- β -cyclodextrin

The formation of inclusion complexes between amoxicillin (AMPC) and 2-hydroxypropyl-β-cyclodextrin (HPCD) was investigated by isothermal microcalorimetry and molecular dynamics simulation to evaluate the inhibitory effects on the degradation of AMPC in aqueous solutions at various pH. The process depended significantly on the ionic species of AMPC in the solution. In a strong acid solution, cationic AMPC and HPCD formed two different types of inclusion complexes with a 1:1 stoichiometry: the first-type had a high association constant K ₁ of 4.0-8.0·10³ M^-1 and included the penam ring of AMPC in the HPCD cavity (Mode I), while the second-type with a K ₂ of 1.0·10³ M^-1 contained the phenyl group of AMPC (Mode II). Furthermore, a complex with a 1:2 (AMPC:HPCD) stoichiometry was realized in a two-step reaction and was characterized by a smaller K _1:2of 4.0·10² M^-1 and larger negative enthalpy and entropy changes than the complexes with a 1:1 stoichiometry. Since the β-lactam ring of AMPC could be protected by inclusion with HPCD in the 1:2 complex and Mode I of 1:1 complexes, the degradation of AMPC in the presence of HPCD was approximately four times slower than in its absence at pH 1.2 and 37°C. In weak acid and neutral solutions, zwitterionic AMPC and HPCD formed only one type of inclusion complex with a 1:1 stoichiometry, where the phenyl group was included (Mode II). AMPC was very stable in these solutions (t _1/2=226 h at pH=6.0) and there is little significant difference in the degradation rate between complexed AMPC and uncomplexed AMPC. Thus, the results indicated that the inclusion complex of AMPC with HPCD, effectively increasing the stability of AMPC in a strong acidic solution like that the stomach, would be useful for eradicating Helicobacter pylori infection and as a drug delivery system. This revised version was published online in July 2006 with corrections to the Cover Date.     

Low coordinate germanium and tin compounds (ArO)2ME and (ArO)2MM′Ln M=Ge, Sn; E=S, Se, –NSiMe3 M′=Cr, W, Fe, Pt [Ar=2,4,6-tris((dimethylamino)methyl)phenyl-]

The reactions of the divalent species (ArO)₂M (Ar=2,4,6-[(CH₃)₂NCH₂]₃C₆H₂; M=Ge, Sn) with either Me₃SiN₃, elemental S₈, Se or transition metal complexes M′(CO)_n+1 (M′=Fe, n=4; M′=Cr, W; n=5) (Ph₃P)₂Pt·C₂H₄ have resulted in the isolation of either the new stable formal metallanimines (ArO)₂M=N–SiMe₃, germanethione, -selone (ArO)₂Ge=E (E=S, Se) (the expected formations of the stannanethione and -selone were not observed), or the (ArO)₂M=M′(CO)_n, (ArO)₂M=Pt(PPh₃)₂ complexes, respectively. The direct oxidation of the (ArO)₂M species with various oxidizing agents led to the formation of the corresponding metalloxanes [(ArO)₂M–O–]₂. All of the chalcogenido- and transition metal–metal 14 complexes have been physicochemically and chemically characterized. The reactions of the (ArO)₂Ge=E (E=S, Se) compounds with 3,5-di-tert-butyl-1,2-benzoquinone produced, by extrusion of sulfur or selenium, the dioxametalloles corresponding to the formal addition of the divalent species (ArO)₂M to the benzoquinone. A substitution reaction of chalcogen (S/Se) has been observed permitting to go from germaneselone to germanethione.     

Intramolecular cyclization of ketene containing both acyl andN-alkylimidoyl substituents. Synthesis and crystal and molecular structure of 3-benzoyl-5-phenyl-2H,4H-furo[3,2-c] isoquinolin-2-one

Thermal decarbonylation of 1-benzyl-4,5-dibenzoyl-2,3-dihydropyrrole-2,3-dione yields benzoyl[N-benzyl(phenylglyoxalimidoyl)]ketene. The latter undergoes intramolecular cyclization to 3-benzoyl-5-phenyl-2,3,4,5-tetrahydrofuro[3,2-c]isoquinolin-2-one. Which is oxidized to 3-benzoyl-5-phenyl-2H,4H-furo[3,2-c]isoquinolin-2-one under the reaction conditions. The crystal and molecular structure of the title compound was studied by X-ray structural analysis. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 563–565, March, 1997.     

The solid state reactions of o-aminobenzoic acid with Zn(Ⅱ), Cu(Ⅱ), Ni(Ⅱ), Mn(Ⅱ) acetate hydrate at room temperature

The solid-solid state reactions of o-aminobenzoic acid with Zn(OAc)2.2H2O, Cu(OAc)2 .H2O, Ni(OAc)2.4H2O and Mn(OAc)2.4H2O result in the formation of corresponding complexes M(OAB)2 (M = Zn(Ⅱ), Cu(Ⅱ), Ni(Ⅱ), Mn(IⅡ)). XRD, IR and elemental analysis methods have been used to characterize the solid products. The activation energies of these reactions, which are calculated from the kinetic data obtained by means of the isothermal electrical conductivity measurement method, have been found to increase in the order: Cu(OAc)2.H2O(37.7 kJ.mol-1)~Mn(OAc)2.4H2O (39.7kJ.mol-1) < Zn(OAc)2.2H2O (56.3 kJ.mol-1) < Ni(OAc)2.4H2O (85.2 kJ.mol-1). The trend is related to their crystal structures.     

A deuteron NMR study of axial motion and side chain conformation in the mesophase of discotic liquid crystal main-chain polymers

Pulsed deuteron NMR spectroscopy has been used to examine the axial motion and the side-chain conformation in both oriented and unoriented mesophases of discotic liquid crystal main-chain polymers based on pentyloxy or heptyloxy substituted triphenylenes. Lineshape simulations show that the rotational motion of the triphenylene rings about the column axes can be described by an inhomogeneous distribution of reorientation angles around 45°. However, only about 60% of the discs are involved in such large amplitude motions; the remaining 40% have reorientation angles below 10°. This illustrates the severe restrictions imposed on the rotation of the discs by the interlinkage of the columns via the alkylene spacers. Furthermore, the simulations demonstrate that, at the -carbon, the side chains show very little fast internal motion, but have a relatively complex conformation involving a disorder which does not change on the microsecond timescale. Since such a disorder is not present in the corresponding monomeric samples it is ascribed to the presence of the spacers. These results are also consistent with the presence of large sterical hindrances between the first side chains segments of adjacent discs, and they indicate a correlated reorientation of the discotic units within a column.     

An approach to channel type molecular structures. 1. Synthesis ofBouquet-shaped molecules based on an [18]-O6 polyether macrocycle

An approach to a transmembrane cation channel is described. It is based on the grafting of oxygen bearing side-chains on a macrocyclic polyether unit that constitutes the organizing core. The resulting species has a structure of overall bouquet shape. The synthesis of such a molecule . _M ⁰ ,14a is described, together with that of its analogue bearing polymethylene side-chains _M ^C ,14b. The physicochemical properties of these molecules indicate that they possess the features expected on the basis of their structure.This paper is dedicated to the memory of the late Dr C. J. Pedersen.     

Capture by stabilized continuum: Classical and quantum aspects

We review here the results of our investigations concerning chaotic atomic scattering in the presence of a laser field. Particular emphasis is put on the existence of classical stable resonance structures, induced by the intense laser field, which are embedded in the field-free continuum. We show that phase space structures in the vicinity of a resonance island play an important role in the chaotic scattering behavior and form the basis for a mechanism to enhance the lifetimes of the collisional partners. Quantum calculations, based on a wave packet propagation method, show that quantum solutions are strongly influenced by the classical phase space structures. More specifically, a wave packet is found to spread differently in the regular and chaotic regions; in the latter case it spreads exponentially with time until saturation occurs, defining the saturation time. We also investigate the dependence of the spreading rates in both the regular and chaotic regimes. Calculations with an ensemble of classical trajectories are also presented to further illustrate the smoothing effects of varying.     

[IrBr6]2-的反对称极化率与圆偏振激光诱导的ESR谱频移

在理论上研究了顺磁性粒子体系的圆偏振激光诱导的ＥＳＲ谱频移效应。给出磁场中分子反对称极化率的公式，并以［ＩｒＢｒ６］＾２－离子为例讨论了吸收带半高宽的影响。计算了［ＩｒＢｒ６］＾２－的ＥＳＲ谱在圆偏振激光作用下的频移。结果发现：在光学共振区附近，ＥＳＲ频移可达１ＭＨｚ的量级，与钠原子体系结果类似。