Novel acyclic nucleoside phosphonate analogues with potent anti-hepatitis B virus activities.

Novel acyclic nucleoside phosphonates with a pyrimidine base preferentially containing an amino group at C-2 and C-4 and a 2-(phosphonomethoxy)ethoxy or (R)-2-(phosphonomethoxy)propoxy group at C-6 selectively inhibit the replication of wild-type and lamivudine-resistant hepatitis B viruses. The activity of the most potent compounds was comparable to that of adefovir.

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.

A subnanomolar inhibitor of human immunodeficiency virus type 1 (HIV-1) protease, designated QF34, potently inhibits the wild-type and drug-resistant enzyme. To explain its broad activity, the binding of QF34 to the wild-type HIV-1 protease is investigated by molecular dynamics simulations and compared to the binding of two inhibitors that are used clinically, saquinavir (SQV) and indinavir (IDV). Analysis of the flexibility of protease residues and inhibitor segments in the complex reveals that segments of QF34 were more mobile during the dynamics studies than the segments of SQV and IDV. The dynamics of hydrogen bonding show that QF34 forms a larger number of stable hydrogen bonds than the two inhibitors that are used clinically. Absolute binding free energies were calculated with molecular mechanics-generalized Born surface area (MM-GBSA) methodology using three protocols. The most consistent results were obtained using the single-trajectory approach, due to cancellation of errors and inadequate sampling in the separate-trajectory protocols. For all three inhibitors, energy components in favor of binding include van der Waals and electrostatic terms, whereas polar solvation and entropy terms oppose binding. Decomposition of binding energies reveals that more protease residues contribute significantly to the binding of QF34 than to the binding of SQV and IDV. Moreover, contributions from protease main chains and side chains are balanced in the case of QF34 (52:48 ratio, respectively), whereas side chain contributions prevail in both SQV and IDV (main-chain:side-chain ratios of 41:59 and 45:55, respectively). The presented results help explain the ability of QF34 to inhibit multiple resistant mutants and should be considered in the design of broad-specificity second-generation HIV-1 protease inhibitors.

The nature of improper, blue-shifting hydrogen bonding verified experimentally.

In the infrared spectra of solutions in liquid argon of dimethyl ether ((CH(3))(2)O) and fluoroform (HCF(3)), bands due to a 1:1 complex between these monomers have been observed. The C-H stretch of the HCF(3) moiety in the complex appears 17.7 cm(-1) above that in the monomer, and its intensity decreases by a factor of 11(2). These characteristics situate the interaction between the monomers in the realm of improper, blue-shifting hydrogen bonding. The complexation shifts the C-F stretches downward by some 9 cm(-1), while the C-H stretches in (CH(3))(2)O are shifted upward by 9-15 cm(-1), and the C-O stretches are shifted downward by 5 cm(-1). These shifts are in very good agreement with those calculated by means of correlated ab initio methods, and this validates a two-step mechanism for improper, blue-shifting hydrogen bonding. In the first step, the electron density is transferred from the oxygen lone electron pairs of the proton acceptor ((CH(3))(2)O) to fluorine lone electron pairs of the proton donor (CHF(3)) which yields elongation of all CF bonds. Elongation of CF bonds is followed (in the second step) by structural reorganization of the CHF(3) moiety, which leads to the contraction of the CH bond. It is thus clearly demonstrated that not only the spectral manifestation of H-bonding and improper H-bonding but also their nature differ.

Interactions between allosteric modulators and 4-DAMP and other antagonists at muscarinic receptors: potential significance of the distance between the N and carboxyl C atoms in the molecules of antagonists.

Allosteric enhancement of the affinity of muscarinic receptors for their ligands offers a new way to influence cholinergic neurotransmission. The structure of the allosteric binding domain(s) and the features of agonists, antagonists and modulators which determine the occurrence of either positive or negative cooperativity require clarification. We tested interactions between allosteric modulators alcuronium, strychnine and brucine and eight antagonists at muscarinic receptors expressed in CHO cells. In experiments with unlabeled antagonists, all three modulators enhanced the affinity for 4-diphenylacetoxy-N-dimethylpiperidinium (4-DAMP) at the M2 receptors, and strychnine did so also at the M4 receptors. Positive interactions were also observed between alcuronium and L-hyoscyamine (M2) and scopolamine (M2), between strychnine and butylscopolamine (M4), L-hyoscyamine (M2 and M4) and scopolamine (M4), and between brucine and scopolamine (M2). Positive effects of alcuronium, strychnine and brucine on the affinity of the M2 receptors for 4-DAMP have been confirmed by direct measurements of the binding of [3H]-4-DAMP. A comparison of molecular models of several antagonists which are esters revealed that antagonists in which the distance between the N and the carboxyl C atoms corresponds to five chemical bonds are more likely to display positive cooperativity with alcuronium at the M2 receptors than the antagonists in which the N-carboxyl C distance corresponds to four chemical bonds.

Single crystals of an ionic anthracene aggregate with a triplet ground state

Crystalline supramolecular aggregates consisting of charged organic molecules, held together through metal-cluster-mediated Coulomb interactions, have attracted interest owing to their unusual structural, chemical and electronic properties. Aggregates containing metal cation clusters 'wrapped' by lipophilic molecular anions have, for example, been shown to be kinetically stable and soluble in nonpolar liquids such as saturated hydrocarbons. The formation of supramolecular aggregates can even be exploited to generate aromatic hydrocarbons that carry four negative charges and crystallize in the form of organic poly(metal cation) clusters or helical polymers. Here we report the anaerobic crystallization of an ionic organic aggregate--a contact ion septuple consisting of a fourfold negatively charged 'tripledecker' of three anthracene molecules bridged by four solvated potassium cations. Its electronic ground state is shown experimentally, using temperature-dependent electron paramagnetic resonance spectroscopy, to be a triplet. Although the spins in this biradical ionic solid are separated by a considerable distance, density functional theory calculations indicate that the triplet ground state is 84 kJ mol(-1) more stable than the first excited singlet state. We expect that the successful crystallization of the ionic solid we report here, and that of a covalent organic compound with a triplet ground state at room temperature, will stimulate further attempts to develop new triplet-ground-state materials for practical use.

The Li(+)-Initiated Twofold Dehydrogenation and C-C Bond Formation of Hexaphenylbenzene to the Dilithium Salt of the 9,10-Diphenyltetrabenz

Partly solvent-separated and partly solvent-shared, the contact ion triple of the 9,10-diphenyltetrabenz[a,c,h,j]anthracene dianion is formed by the ultrasonically activated reaction of hexaphenylbenzene with lithium metal powder in 1,2-dimethoxyethane (dme) [Eq. (1)]. The proposed microscopic pathway for this reaction-twofold dehydrogenation and C-C bond formation-is supported by quantum-chemical calculations.

Quantum chemical calculation of the (S)-9-(2,3-dihydroxypropyl)adenine molecule.

Quantum chemical calculations of conformational maps of the molecule of a new virostatic agent (S)-9-(2,3-dihydroxypropyl)adenine were performed. The thermodynamically most advantageous conformation I corresponds, for the D-series, to the alpha-ribo configuration, while the following minima, which are close in energy (II,III), correspond to beta-ribo and beta-xylo configurations.