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.     

The electron—ion recombination coefficient in CO2 and NH3. Deviations from a linear density dependence at elevated pressures

The rate coefficient for electron—ion recombination at 292 K rises to a value of 7 x 10^?5 cm³ s^?1 in CO₂ at 13 x 10¹⁹ molecule cm^?3, but is non-linear with density above 8 x 10¹⁹ molecule cm^?3. In ammonia it passes through a definite maximum of 7 x 10^?5 cm³ s^?1 at 2.4 x 10¹⁹ molecule cm^?3     

Experimental and theoretical study of the V → T,R relaxation of CD4 between 300 and 100 K

Rate constants for the vibrational deactivation of CD₄ by the collision partners CD₄, He, Ne, Ar, Kr, D₂ and O₂ have been measured using a laser-fluorescence technique. The results are compared with those for the deactivation of CH₄ by the same collision partners and with a modified SSH type theoretical treatment.     

An investigation of the complexation of host <Emphasis Type="Italic">N,N′</Emphasis>-bis(9-phenyl-9-thioxanthenyl)ethylenediamine with dihaloalkane guests

In this study, the formation of supramolecular inclusion complex of doxorubicin (DOX), a high loading and pH-dependent delivery of DOX on β-CD dendrimer was studied. β-cyclodextrin (β-CD) dendrimer having β-CD in both periphery and core was prepared with entrapment efficiency using click reaction. The encapsulation property of the β-CD-dendrimer was investigated by DOX as model drug. The chemical construction of β-CD-dendrimer was described by ¹H NMR, ¹³C NMR and FTIR and its inclusion complex construction was studied by FTIR, DSC, SEM, and DLS techniques. It was confirmed that β-CD dendrimer able to encapsulate DOX in solution; as a result, the designed complex revealed pH-dependent sustained release of DOX, in vitro. Also, the in vitro outcomes on T47D cells displayed that complexation of DOX with β-CD dendrimer involved an improvement of in vitro cytotoxicity and anticancer activity and this data appeared to be as a result of the developed solubility of the DOX.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Supplementary d and f functions in molecular wave functions: Optimum and nonoptimum exponents

Energy optimization calculations have been carried out to determine the variability of optimum p, d, and f polarization function exponents in molecules containing first- and second-row elements and in normal valency and hypercoordinate species. Optimum exponents were determined for single sets of higher-order functions at both Hartree–Fock and correlated (Moller–Plesset) levels of theory using the Dunning–Hay double zeta and the McLean–Chandler triple zeta basis sets. More detailed calculations were used to test the response to nonoptimum d and f function exponents of the total energy, the optimum geometry, and harmonic stretching frequencies. The variability in optimum exponents and the size of the energy penalties incurred by adopting nonoptimum values reduces the utility of standard exponents for p, d, and f polarization functions. © 1993 John Wiley & Sons, Inc.     

Computational convergence of electronic structure calculations of transition metal ligand complexes

Calculations of binding energies and optimum geometries of compounds of the series M(H₂O)⁺ with M = Sc to Zn have been carried out and compared with gas-phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree–Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d-function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d-function space. However, MP2 or higher-level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas-phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.     

A PULSED LASER AND PULSE RADIOLYSIS STUDY OF AMPHIPHILIC CHLOROPHYLL DERIVATIVES WITH PDT ACTIVITY TOWARD MALIGNANT MELANOMA

Two amphiphilic derivatives of chlorophyll, which have high potential as photodynamic therapy sensitizers for malignant melanoma have been investigated by a combination of laser flash photolysis and pulse radiolysis. It is shown that direct excitation of monomeric forms of these molecules in both hydrophilic and hydrophobic environments produces significant yields of the corresponding triplet states, which have been characterized in terms of spectral and kinetic parameters. In both environments, scavenging of the triplets by oxygen produces singlet oxygen, O₂(^lΔ₈), with essentially unit efficiency as evidenced by time-resolved IR luminescence measurements.     

Synthesis of macrocyclic polystyrene-polydimethylsiloxane block copolymers

A series of macrocyclic polystyrene (PS)-polydimethylsiloxane (PDMS) block copolymers and similar block copolymers was synthesized by sequential polymerization of styrene and hexamethyl cyclotrisiloxane (D₃) initiated by a difunctional anionic initiator in THF at −78° followed by coupling with Cl₂SiMe₂ in very dilute (10⁻⁵ – 10⁻⁶ M) solutions. Total molecular weights ranged from about 2–85 × 10³. The formation of monodisperse macrocyclic block copolymers was indicated by the lower (15–30%) hydrodynamic volume of the rings compared to that of the linear block copolymers. Carbon-13 and ²⁹Si NMR likewise supported the absence of linear polymer in the macrocyclic block copolymer. The behavior of second virial coefficient A₂ of the rings and the linears versus temperature was examined by static light scattering in cyclohexane. Below 20° the A₂ for the linear polymer goes negative while that for the cycle remains positive. Dynamic light scattering (DLS) as a function of temperature also reflects that the cyclic polymers remain well solvated even down to 12°C. The DLS autocorrelation functions for the linear triblock however demonstrate the onset of aggregation and phase separation as the temperature is reduced below 20°C.