Lipophilicity in PK design: methyl, ethyl, futile

Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume of distribution. However, more lipophilic compounds also become more vulnerable to P450 metabolism, leading to higher clearance. Molecular size and hydrogen bonding capacity are two other properties often considered as important for membrane permeation and pharmacokinetics. Interrelationships among these physicochemical properties are discussed. Increasing size (molecular weight) often gives higher potency, but inevitably also leads to either higher lipophilicity, and hence poorer dissolution/solubility, or to more hydrogen bonding capacity, which limits oral absorption. Differences in optimal properties between gastrointestinal absorption and uptake into the brain are addressed. Special attention is given to the desired lipophilicity of CNS drugs. In examples using -blockers, Ca channel antagonists and peptidic renin inhibitors we will demonstrate how potency and pharmacokinetic properties need to be balanced.     

Purification by HPLC and the UV/Vis absorption spectra of the nitrogen-containing incar-fullerenes iNC60, and iNC70

We report the purification of the nitrogen-containing incar-fullerenes iNC(60) and iNC(70), and their characterisation by UV-Vis absorption spectroscopy.     

An improved synthesis of cyclopropanes from stabilized phosphonates and 1,2-dioxines

Addition of stabilized Horner-Wadsworth-Emmons (HWE) phosphonates to substituted 1,2-dioxines leads to diastereomerically pure di- and trisubstituted cyclopropanes in high yields and represents a viable alternative to ylides in the cyclopropanation reaction involving 1,2-dioxines. While yields are comparable, reaction times with these stabilized phosphonates were accelerated and the diastereoselectivity for this cyclopropanation reaction was significantly greater than for the previously reported examples employing ylides.     

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins

The classical simplex method is extended into the Semiglobal Simplex (SGS) algorithm. Although SGS does not guarantee finding the global minimum, it affords a much more thorough exploration of the local minima than any traditional minimization method. The basic idea of SGS is to perform a local minimization in each step of the simplex algorithm, and thus, similarly to the Convex Global Underestimator (CGU) method, the search is carried out on a surface spanned by local minima. The SGS and CGU methods are compared by minimizing a set of test functions of increasing complexity, each with a known global minimum and many local minima. Although CGU delivers substantially better success rates in simple problems, the two methods become comparable as the complexity of the problems increases. Because SGS is generally faster than CGU, it is the method of choice for solving optimization problems in which function evaluation is computationally inexpensive and the search region is large. The extreme simplicity of the method is also a factor. The SGS method is applied here to the problem of finding the most preferred (i.e., minimum free energy) solvation sites on a streptavidin monomer. It is shown that the SGS method locates the same lowest free energy positions as an exhaustive multistart Simplex search of the protein surface, with less than one-tenth the number of minizations. The combination of the two methods, i.e.. multistart simplex and SGS, provides a reliable procedure for predicting all potential solvation sites of a protein.     

Bond lengthening and through-bond interactions in p,p'-dibenzene and related molecules

The structure of p,p'-dibenzene (PDB) has been investigated by full geometry optimizations using the empirical force field (EFF) and MINDO/3 methods. While other structural parameters are in good agreement, the central bond length calculated by MINDO/3 (1.595 Å), as confirmed by an ab initio (STO-3G basis set) optimization (1.596 Å), is in striking contrast to the corresponding length calculated by EFF (1.543 Å). A detailed analysis of the electronic structure of PDB based on a quantitative perturbational molecular orbital treatment reveals that through-bond coupling of the four π systems is responsible for an elongation of the σ bond which mediates this interaction. Further studies using the EFF and MINDO/3 approaches demonstrate that extended C-C single bonds can arise even in structures with fewer than four π systems. The effect of substituents on the central bond length in PDB has been briefly investigated. (MINDO/3). A variety of other structures have been identified in which bond lengthening may result from through-bond coupling.     

A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor

GABA(C) (rho) receptors are members of the Cys-loop superfamily of neurotransmitter receptors, which includes nicotinic acetylcholine (nACh), 5-HT(3), and glycine receptors. As in other members of this family, the agonist binding site of GABA(C) receptors is rich in aromatic amino acids, but while other receptors bind agonist through a cation-pi interaction to a tryptophan, the GABA(C) binding site has tyrosine at the aligning positions. Incorporating a series of tyrosine derivatives at position 198 using unnatural amino acid mutagenesis reveals a clear correlation between the cation-pi binding ability of the side chain and EC(50) for receptor activation, thus demonstrating a cation-pi interaction between a tyrosine side chain and a neurotransmitter. Comparisons among four homologous receptors show variations in cation-pi binding energies that reflect the nature of the cationic center of the agonist.     

THE REDUCTION AND QUENCHING OF PHOTOEXCITED FLAVINS BY EDTA

Riboflavin was irradiated anaerobically in aqueous EDTA solutions over the pH range 2.5–10. In other dye systems (Bonneau and Pereyre, 1975), only the trivalent anion of EDTA was found to have significant reactivity for photoreduction. For riboflavin, the reactivity begins with monoanionic EDTA, and the reactivity is markedly increased as the charge increases. This suggests that the charge on the reductant is more important to the electron transfer process for riboflavin than the formation of a nonhydrogen bonded nitrogen site on EDTA. At high concentrations of EDTA in the pH range 4–8, quenching of the photoreduction occurs, which can be explained by an energy transfer between the excited singlet state of riboflavin and trianionic EDTA, possibly as an association complex. The rate constants for the photoreduction of riboflavin by the monovalent, divalent, and trivalent anions of EDTA are 1.0 times 10⁷M^-1 s^-l, 4.8 times 10′M^-1 s^-l, and 2.0 times 10⁸M^-1s^-1, respectively. The rate constant for the singlet state quenching by trianionic EDTA is 3 times 10⁹M^-l s^-1, and the limiting quantum yield for intersystem crossing for riboflavin in aqueous solution is 0.50 ± 0.05.     

Graph-theoretical analysis of the bonding topology in polyhedral organic cations

It is shown that in several cases where planar delocalisation in organic cations would result in the formation of an anti-aromatic system, polyhedral delocalisation is the form of bonding actually preferred. This explains, for instance, why organic cations in such cases adopt cage-like structures. A full graph-theoretical analysis, similar to one previously published¹² for polyhedral boranes, carboranes and metal clusters, indicates that the nido structure for (CH)₅⁺ may readily be accounted for. Moreover, in the case of the dication (CH)₆²⁺ the fact that its energy minimum also corresponds to a nido structure is explained. In fact, no closo- or arachno-type structures appear to be possible for organic cations. A number of structural predictions concerning these species are given in the conclusion.     

E-1,2-Dichlorovinyl ethers as irreversible protease inhibitors

The synthesis of a novel motif for threonine protease inhibition is described. The desired E-1,2-dichlorovinyl ethers are obtained from alcohols and trichloroethylene as single diastereomers. Aqueous treatment at pH 11 unmasks the hidden α-chloroacetate, which is required for the reaction with the active site of the protease.     

Application of the NT solvent nucleophilicity scale to attack at phosphorus: solvolyses of N,N,N',N'-tetramethyldiamidophosphorochloridate

The specific rates of solvolysis of N,N,N',N'-tetramethyldiamidophosphorochloridate have been measured at 25.0 degrees C in 31 solvents. Analysis with the extended Grunwald-Winstein equation leads to sensitivities toward changes in solvent nucleophilicity (l) of 1.20 +/- 0.07 and toward changes in solvent ionizing power (m) of 0.69 +/- 0.04. The correlation is improved by omission of the four data points for 2,2,2-trifluoroethanol-ethanol mixtures (F-test value from 155 to 320) with very small reductions in both l and m values. Activation parameters are reported for eight of the solvolyses. The l and m values are very similar to those previously reported for solvolyses of several arenesulfonyl chlorides, consistent with a concerted substitution process. This assignment is supported by a large k(Cl)/k(F) ratio for hydrolysis and a corresponding ratio for hydroxide-assisted hydrolysis of 178. The stereochemistry of nucleophilic attack at tetracoordinate phosphorus(V) is discussed.