A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K.     

A new approach to intermolecular forces in non-bonding regions

A new method to compute intermolecular energies in non-bonding regions is presented. It is based on the assumption that in such regions molecules can be reviewed as the sum of distorted, possibly overlapping, and electron exchanging atoms. The intermolecular energy change at a given distance is due to the sum of the atomic energy changes caused by these distortions. The energy change of any particular atom is computed in a Hartree—Fock model in which the effect of the other atom is represented by an effective potential. This potential in turn is computed from a calculation at a slightly larger intermolecular distance of the potential seen by an external electron in the field of the “other” atom. This potential computed in the RPA approximation and involves the distorted Hartree—Fock orbitals of the other atom (computed in a similar manner to the above) and the RPA response function of the other distorted atom.     

Obtaining partial widths from siegert wavefunctions

It is shown that a simple expression for the partial widths in a multichannel decay problem can be readily obtained from a Siegert wavefunction.     

Determination of residues of pirimicarb and its desmethyl and desmethylformamido metabolites in fruits and vegetables by liquid chromatography-electrospray/mass spectrometry

A method was developed for the simultaneous determination of residues of pirimicarb (I) and its desmethylformamido (II) and desmethyl (III) metabolites in plums, peas, green beans, broad beans, carrots, and swedes. The compounds were extracted with ethyl acetate and determined, without cleanup, by reversed-phase liquid chromatography and electrospray mass spectrometry (MS). MS and MS/MS were used concurrently to monitor the protonated molecules and their common collision-induced dissociation product. The limit of detection (signal-to-noise ratio of >3) was 1 ng/mL, corresponding to crop concentrations of <0.0015 mg/kg. All 3 compounds were determined in plums, broad beans, and green beans by MS without interference. Interferences which affected the determination of desmethylformamido-pirimicarb in peas, and to a lesser extent in carrots and swedes, were eliminated by MS/ MS. Recoveries for all 3 compounds, at 0.05 mg/kg for plums and 0.005 mg/kg for other commodities, were in the range 83-124%. No interconversion of I, II and III, occurred during extraction, and the compounds were stable in extracts for > or = 7 days under appropriate conditions.     

“Dibutylmagnesium”, a convenient reagent for the synthesis of useful organic magnesium reagents MgA2 including cyclopentadienyls,aryloxides, and amides. Preparation of Zr(C5H5)Cl3. X-ray structure of [Mg{μ-N(SiMe)3C6H4N}(SiMe3)-o(OEt2)]2

n-Heptane-soluble “di-butylmagnesium” (I) (a commercially available material, prepared by addition of LiBu^s to MgBuⁿCl, and subsequent addition of ca. 5% MgOct₂ⁿ) has been found to be a useful starting material for obtaining numerous organic magnesium compounds. This is illustrated by its reaction with a number of protic compounds HA to give in good yields Mg(C₅H₅)₂, Mg(C₅H₄Me)₂, or the new compounds MgA₂: IV (A = C₅H₄SiMe₃), V [A = C₅H₃(SiMe₃)₂], VII (A = OC₆H₂Bu₂^t-2,6-Me-4), and X [A₂ = N(SiMe₃)C₆H₄N(SiMe₃)-o(OEt₂)]. The value of such compounds MgA₂ as mild ligand transfer reagents is illustrated by the synthesis of Zr(C₅H₃X₂)Cl₃ (X = H or SiMe₃). Compound X was isolated from OEt₂ solution as the crystalline dimer

with two o-$\text{N}$(SiMe₃)C₆H₄$\text{N}$(SiMe₃) ligands bridging two magnesium atoms and a terminal OEt₂ ligand completing a distorted tetrahedral environment around each Mg. Some key parameters are: MgN_t 1.997(7), MgN_b 2.083(8), MgO 2.041(7) Å; OMgN_t 112.1(3), OMgN_b 119.7(3), and N_tMgN_b 118.5(3)°.     

Comparison of micro- and mesoporous inorganic materials in the uptake and release of the drug model fluorescein and its analogues

The uptake of the three species of the drug model fluorescein (fluorescein sodium salt (FNa), fluorescein free acid (F), and fluorescein diacetate (FDA)) by zeolite NaX and the mesoporous zeotype MCM-41 was investigated as well as their release rates into solutions at pH 7 and pH 4.5. UV/Vis analysis was carried out at a wavelength of 490 nm. Uptakes of the sodium salt of 9 % for zeolite X and 14 % for MCM suggest little penetration of the pores. The use of ethanol as the loading solvent for F resulted in little uptake for both zeolitic materials due to the successful competition of the ethanol for binding sites. Use of acetone (weaker proton acceptor) as loading solvent significantly improved the uptake of F to 17 % and 12 % for zeolite X and MCM, respectively, whilst the uptake of FDA in acetone increased still further to 22 % and 17 % for zeolite X and MCM, respectively. Generally there was a large initial release of the fluorescein analogues from the surface of the zeolites with very little further increase over time. The prescence of an esterase enzyme in the release medium of FDA tripled the release from MCM to 15 % but left the release from zeolite X unaffected at 6 %. The results obtained show that uptake of fluorescein and its analogues is dependent on the loading solvent used, the amount released is influenced by not only the solvent but the pH and the presence of enzymes in the release medium.     

Evidence for the S(N)2' mechanism in hydrolysis of C60F48: origin of the stability of trannulenes

The products of hydrolysis of C60F48 (which contains six isolated double bonds) by either aq. acetone or aq. THF show that no more than twelve fluorines are replaced through nucleophilic substitution, as predicted by the recently identified S(N)2' mechanism. Subsequent HF elimination gives fragments containing a maximum of six epoxide oxygens. Calculated heats of formation of models for the possible initial hydroxy derivatives indicate that there is little energetic discrimination between them, so that a complex mixture is likely to be formed. Overall the data show that hydrolytic degradation of fluorofullerenes is less severe than believed previously, requires a specific motif, and explains the low susceptibility of C60F18 towards hydrolysis and the high stability of trannulenes.