Mechanism of the antigen formation of carvone and related alpha, beta-unsaturated ketones.

In the present study, the mechanism for the antigen formation of alpha, beta-unsaturated ketones was investigated. A series of analogues of carvone ((5R)-5-isopropenyl-2-methyl-2-cyclohexenone) with altered chemical reactivity and with retained overall structure or with retained reactivity and altered three-dimensional structure were synthesized. These analogues were tested for cross-reactivity in carvone-sensitized animals. Cross-reactivity was observed for analogue 3 ((5R)-5-isopropyl-2-methyl-2-cyclohexen-1-one). No cross-reactions were observed for analogues 1 ((2R,5R)-5-isopropenyl-2-methyl cyclohexanone) and 4 ((5R)-2,3-dimethyl-5-isopropenyl-2-cyclohexene-1-one). Both those compounds also failed to induce sensitization. These findings demonstrate that alpha, beta-unsaturated ketones form antigens after a nucleophilic attack at the beta-carbon with soft nucleophiles such as thiol in cysteine and not with the formation of a Schiff's base after a nucleophilic attack at the carbonyl carbon with nitrogen nucleophiles. Furthermore, no cross-reactivity was observed between R- and S-carvone indicating the importance of the 3-dimensional structure of haptens (and antigens) in T-cell recognition. The analogues were also tested for cross-reactivity on patients allergic to carvone. The results from the animal study were confirmed.

Experimental and computational screening models for the prediction of intestinal drug absorption.

The aim of this study was to devise experimental protocols and computational models for the prediction of intestinal drug permeability. Both the required experimental and computational effort and the accuracy and quality of the resulting predictions were considered. In vitro intestinal Caco-2 cell monolayer permeabilities were determined both in a highly accurate experimental setting (Pc) and in a faster, but less accurate, mode (Papp). Computational models were built using four different principles for generation of molecular descriptors (atom counts, molecular mechanics calculations, fragmental, and quantum mechanics approaches) and were evaluated for their ability to predict intestinal membrane permeability. A theoretical deconvolution of the polar molecular surface area (PSA) was also performed to facilitate the interpretation of this composite descriptor and allow the calculation of PSA in a simplified and fast mode. The results indicate that it is possible to predict intestinal drug permeability from rather simple models with little or no loss of accuracy. A new, fast computational model, based on partitioned molecular surface areas, that predicts intestinal drug permeability with an accuracy comparable to that of time-consuming quantum mechanics calculations is presented.

Caco-2 monolayers in experimental and theoretical predictions of drug transport.

This review examines the use of Caco-2 monolayers in the prediction of intestinal drug absorption. First, the different routes of drug transport in Caco-2 monolayers are compared with those seen in vivo. Second, the prediction of drug absorption in vivo from transport experiments in cell monolayers is discussed for different classes of drugs. Finally, the use of Caco-2 monolayers as a reference model in physico-chemical and theoretical predictions of drug absorption is discussed. We conclude that Caco-2 monolayers can be used to identify drugs with potential absorption problems, and possibly also to select drugs with optimal passive absorption characteristics from series of pharmacologically active molecules generated in drug discovery programs.

Structural analogues inhibit the sensitizing capacity of carvone.

The aim of the study was to investigate the effect of non-allergenic structural analogues on the sensitizing potential of carvone, a fragrance allergen. The possibility that one molecule might inhibit the allergenic activity of another molecule has been debated for 25 years. The Research Institute for Fragrance Materials states that the sensitizing activity from certain fragrance aldehydes is "quenched" by the addition of other specific chemicals. However, other studies do not confirm the results, although several attempts have been made. We used a guinea pig method designed to study the sensitizing capacity of fragrance allergens. Induction was performed with either carvone alone or with a mixture of carvone and one of two analogues. A significant difference in the response rates (p < 0.001) was observed between the animals induced with carvone alone and those induced with any of the mixtures. Our investigation shows that by using selected molecules it is possible to significantly reduce the sensitizing effect of a fragrance allergen.

Virtual screening of intestinal drug permeability.

Lead compounds generated in high throughput drug discovery programmes often have unfavorable biopharmaceutical properties, resulting in a low success rate of such drug candidates in clinical development. Drug companies and researchers would thus like to have methods of predicting biopharmaceutical properties accurately. The intestinal permeability to a lead compound is one such property which is particularly important. Therefore, access to methods to accurately predict biopharmaceutical properties, such as the intestinal permeability of a large series of compounds, is of particular importance. This review deals with new theoretical methods used to predict intestinal drug permeability. There are several possible transport routes across the intestine, but theoretical methods generally deal with only one of them, the passive transcellular route. Therefore, this review will also discuss the relative importance of passive and active drug transport and efflux routes using recent data generated in cell cultures, animal models and human subjects.

Prediction of the intestinal absorption of endothelin receptor antagonists using three theoretical methods of increasing complexity.

PURPOSE: Three new computational strategies have been evaluated for their ability to predict intestinal membrane permeability to a series of endothelin receptor antagonists. METHODS: The three methods were evaluated using a set of ten nonpeptide endothelin receptor antagonists. The simplest method, "the rule of five", is based on 2D parameters such as the number of potential hydrogen bonds, molecular weight and calculated lipophilicity. A method based on molecular mechanics calculations is used to calculate 3D parameters such as polar and non-polar parts of the molecular surface area. The third method uses quantum mechanics to calculate molecular properties related to the valence region. RESULTS: Descriptors derived by the latter two methods correlated well with permeability coefficients of the endothelin receptor antagonists. On the other hand, the rule of five failed to discriminate between drugs with high and low permeability. CONCLUSIONS: Molecular surface descriptors and descriptors derived from quantum mechanics are potentially useful for the virtual screening of the permeability of the intestinal membrane to endothelin receptor antagonists.

Design, synthesis, and evaluation of Phe-Gly mimetics: heterocyclic building blocks for pseudopeptides.

Enantiopure heterocyclic Boc-protected Phe-Gly dipeptidomimetics containing 1,3,4-oxadiazole, 1,2,4-oxadiazole, and 1,2,4-triazole ring systems have been synthesized as building blocks in the synthesis of pseudopeptides. Three derivatives (1-3) have the carboxylic acid function directly bound to the heterocyclic ring, and three derivatives (4-6) have an extra methylene group between the heterocyclic ring and the acid function to allow for an increased conformational flexibility. The mimetics were used as Phe-Gly replacements in the biologically active peptides dermorphin (Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH(2)) and substance P (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-MetNH(2), SP). The pseudopeptide synthesis was performed using solid-phase methodology on a MBHA-resin using Boc-chemistry. The biological evaluation was performed by testing the micro- and delta-opioid receptor affinities of the dermorphin pseudopeptides and the NK(1) receptor affinities of the SP pseudopeptides. The results showed that all mimetics except 3 were excellent replacements of Phe-Gly in dermorphin since they displayed affinities for the micro-receptor (IC(50) = 12-31 nM) in the same range as dermorphin itself (IC(50) = 6.2 nM). The agonist activity of three pseudopeptides at human micro-receptors was also evaluated. It was shown that the tested compounds retained their agonist activity. The SP pseudopeptides showed considerably lower affinities (IC(50) > 1 microM) for the NK(1) receptor than SP itself (IC(50) = 1.5 nM) indicating that the Phe-Gly replacements prevent the pseudopeptides from adopting bioactive conformations.

Effect of molecular charge on intestinal epithelial drug transport: pH-dependent transport of cationic drugs.

The aim of this study was to investigate the effect of ionization on drug transport across the intestinal epithelium in order to include this effect in structure-absorption relationships. The pH-dependent permeation of one rapidly (alfentanil) and one slowly (cimetidine) transported basic model drug across Caco-2 cell monolayers was investigated. Both drugs had pK(a)values in the physiological pH range. The permeability coefficients (P(c)) of the model drugs were obtained at varying apical buffer pHs, thus varying the degree of drug ionization (from 5 to 95%). The relationship between P(c) and the fraction of the drug in un-ionized form (f(u)) was analyzed to delineate the permeability coefficients of the un-ionized (P(c,u)) and ionized (P(c,i)) forms of the drugs. Theoretical estimates of the pK(a) values were also calculated from ionization energies for each model compound. For both drugs, a linear increase in P(c) was observed with increasing f(u). Transport of the un-ionized form was 150- and 30-fold more rapid than transport of the ionized form for alfentanil and cimetidine, respectively. However, when f(u) <0.1, the contribution of the ionized form was significant. Because f(u) is <0.1 over the entire physiological pH range for a large number of drugs, these results will have implications on predictions of in vivo intestinal drug absorption both from in vitro studies in cell cultures and from computed structural properties of drug molecules.

Prediction of membrane permeability to peptides from calculated dynamic molecular surface properties.

PURPOSE: To develop a theoretical method for prediction of transcellular permeability to peptides. METHODS: The dynamic molecular surface properties of 19 oligopeptide derivatives, divided into three homologous series were calculated. The dynamic molecular surface properties were compared with commonly used experimental predictors of membrane permeability such as partition coefficients. Relationships between the dynamic molecular surface properties and intestinal epithelial permeability, as determined in Caco-2 cell monolayers, were used to develop a model for prediction of the transmembrane permeability to the oligopeptide derivatives. RESULTS: A theoretical model was derived which takes both the polar and non-polar part of the dynamic molecular surface area of the investigated molecule into consideration. The model provided a strong relationship with transepithelial permeability for the oligopeptide derivatives. The predictability of transepithelial permeability from this model was comparable to that from the best experimental descriptor. CONCLUSIONS: To our knowledge, this is the first example of a theoretical model that gives a satisfactory relationship between calculated molecular properties and epithelial permeability to peptides by accounting for both the hydrogen bonding capacity and the hydrophobicity of the investigated molecule. This model may be used to differentiate poorly absorbed oligopeptide drugs at an early stage of the drug discovery process.

Synthesis and Use of Pseudopeptides Derived from 1,2,4-Oxadiazole-, 1,3,4-Oxadiazole-, and 1,2,4-Triazole-based Dipeptidomimetics.

This chapter focuses on the isosteric replacement of peptide bonds with three different types of heterocyclic ring systems (1); 1,2,4-oxadiazole (2), 1,3,4-oxadiazole (3), and 1,2,4-triazole rings (4-6). The ring systems are similar in size and shape but show variations in aromatic, electrostatic, and hydrogen bonding properties. These variations provide opportunities to study properties of importance for amide bond mimicry. The derivatives are synthesized from protected natural amino acids, and the reaction conditions have been chosen so that the enantiopurity is retained during the reaction sequences. Two series of mimetics will be described, one in which the carboxylic acid functionality is directly attached to the heterocyclic ring (1) and one series with a methylene group inserted between the ring and the carboxylic acid group (7). Since we have focused on the design and synthesis of Phe-Gly mimetics, the synthetic examples described here start from L: -phenylalanine. However, we have used the same synthetic scheme also for other amino acids and notes will be given when other derivatives require differences in reaction conditions (1). The use of the dipeptidomimetics as building blocks in pseudopeptide synthesis will also be described (7). These syntheses are performed on solid phase using Boc-chemistry. Also, the deprotection and purification of the pseudopeptides by reversed phase HPLC will be discussed.

Evaluation of dynamic polar molecular surface area as predictor of drug absorption: comparison with other computational and experimental predictors.

The relationship between various molecular descriptors and transport of drugs across the intestinal epithelium was evaluated. The monolayer permeability (Pc) of human intestinal Caco-2 cells to a series of nine beta-receptor-blocking agents was investigated in vitro. The dynamic polar molecular surface area (PSAd) of the compounds was calculated from all low-energy conformations identified in molecular mechanics calculations in vacuum and in simulated chloroform and water environments. For most of the investigated drugs, the effects of the different environments on PSAd were small. The exception was H 216/44, which is a large flexible compound containing several functional groups capable of hydrogen bonding (PSAd,chloroform = 70.8 A2 and PSAd,water = 116.6 A2). The relationship between Pc and PSAd was stronger than those between Pc and the calculated octanol/water distribution coefficients (log Dcalc) or the experimentally determined immobilized liposome chromatography (ILC) retention. Pc values for two new practolol analogues and H 216/44 were predicted from the structure-permeability relationships of a subset of the nine compounds and compared with experimental values. The Pc values of the two practolol analogues were predicted well from both PSAd calculations and ILC retention studies. The Pc value of H 216/44 was reasonably well-predicted only from the PSAd of conformations preferred in vacuum and in water. The other descriptors overestimated the Pc of H 216/44 100-500-fold.

Polar molecular surface properties predict the intestinal absorption of drugs in humans.

PURPOSE: A theoretical method has been devised for prediction of drug absorption after oral administration to humans. METHODS: Twenty structurally diverse model drugs, ranging from 0.3 to 100% absorbed, were investigated. The compounds also displayed diversity in physicochemical properties such as lipophilicity, hydrogen bonding potential and molecular size. The dynamic molecular surface properties of the compounds were calculated, taking into account their three-dimensional shape and flexibility. RESULTS: An excellent sigmoidal relationship was established between the absorbed fraction after oral administration to humans (FA) and the dynamic polar molecular surface area (PSAd) (r2 = 0.94). The relationship was stronger than those obtained for more established predictors of drug absorption. Drugs that are completely absorbed (FA > 90%) had a PSAd < or = 60 A2 while drugs that are < 10% absorbed had a PSAd > or = 140 A2. CONCLUSIONS: The results indicate that PSAd can be used to differentiate poorly absorbed drugs at an early stage of the drug discovery process.

Design, synthesis, tandem mass spectrometric sequencing and biological activity of NGF mimetics.

Nine low molecular weight nerve growth factor (NGF)-like peptides have been designed to mimic the putative receptor-binding epitope of NGF defined by two beta-hairpin loops. Eight different spacers were used as variable links between the beta-loop amino acid residues, which from mutagenesis experiments were found to play an important role in the biological activity of NGF. These spacers were amino acids, natural or non-natural, differing in length (5-13 A) and polarity. The peptides were synthesized via the Fmoc solid-phase peptide synthesis and purified by reversed-phase HPLC. Their primary sequences were analyzed by a combination of automated Edman degradation and mass spectrometry. The peptides were tested using two different biological assays, the fibre outgrowth from chick embryonic sympathetic ganglia and the PC12 cell differentiation assay. Weak antagonistic effects could be observed for some peptides.

Correlation of drug absorption with molecular surface properties.

The correlation between dynamic surface properties of drug molecules and drug absorption in two common in vitro models of the intestinal wall (Caco-2 monolayers and rat intestinal segments) has been investigated. A homologous series of beta-adrenoreceptor antagonists were used as model compounds. Dynamic molecular surface properties, considering all low-energy conformations, of the compounds were calculated. The flexibility of the molecules was studied by molecular mechanics calculations (MM2) and the van der Waals' (vdW), and water accessible surface areas were calculated and averaged according to a Boltzmann distribution. Excellent correlations were obtained between the dynamic polar vdW surface areas and cell permeabilities in Caco-2 cells and rat ileum (r2 = 0.99 and 0.92, respectively). These correlations were stronger than those between calculated octanol/buffer partition coefficients (log Doct,7.4) and permeability (r2 = 0.80 and 0.73, respectively). Moreover, the calculated log Doct,7.4 values failed to rank the permeability coefficients through Caco-2 monolayers and rat ileum in the correct order. The results indicate that dynamic polar surface area is a promising alternative model for the prediction of oral drug absorption.

Synthesis of C-(beta-D-glycosyl) analogues of 3-deoxy-D-manno-2-octulosonic acid (Kdo) as potential inhibitors of CMP-Kdo synthetase.

Eight C-(beta-D-glycosyl) analogues (14-21) of Kdo (3-deoxy-D-manno-2-octulosonic acid) were obtained from isopropylidene-protected ester precursors and tested in vitro for their inhibitory activity on CMP-Kdo synthetase. None had more than minor inhibitory activity.

Sequence dependence of DNA structure. The B, Z, and A conformations of polydeoxynucleotides containing repeating units of 6 to 16 base pairs.

In order to study the sequence dependence of the B-Z transition, we have synthesized eight double-stranded polydeoxynucleotides. The polymers have defined alternating purine-pyrimidine sequences with repeating units of 6-16 base pairs, and contain 12.5-33% AT base pairs. A and T nucleotides are in nearest-neighbor positions in the series poly[d[TA(CG)2-7]], but are isolated from each other, with minimum separations of 2 and 6 GC base pairs, in poly[d[TGCA(CG)6]] and poly[T(GC)3A(CG)4)]], respectively. All of the polymers except poly[d[TA(CG)2]] were shown by circular dichroism to undergo a right- to left-hand helical transition at high NaCl concentrations, and all polymers exhibited a B to A transition in the presence of ethanol. Poly[d[TA(CG)7]] was the only polymer to undergo a B to Z to A transition in ethanol. At a constant percentage of AT base pairs, the B-Z transition is sequence-dependent, occurring at lower salt concentrations for polymers containing longer runs of contiguous GC base pairs in the repeating unit.

Structural analysis of two 2-deoxy analogues of alpha- and beta-KDO and the methyl alpha- and beta-glycosides of KDO, and determination of their metal-ion-binding properties.

Ammonium 2,6-anhydro-3-deoxy-D-glycero-D-talo-octonate (1), a potent inhibitor of the enzyme CMP-KDO synthetase, its C-2 epimer 2, and the methyl beta- (3) and alpha-glycoside (4) of KDO were studied by 1H- and 13C-n.m.r. spectroscopy. Compound 1 was also analysed by X-ray crystallography. Each compound adopted a 5C2 chair conformation with the side chain equatorial. The preponderant side-chain conformation of 1 in solution was the same as that in the crystal and was stabilised by an intramolecular hydrogen bond from HO-8 to the carboxylate group. This hydrogen bond appeared to be present also in 3. However, the side-chain conformation of 2 and 4 was different from that in 1 and 3. The metal-ion-binding properties, determined on the basis of the line-broadening effects of Mn2+ on the 13C-n.m.r. signals, showed that the carboxylate group was involved in the binding with O-8 in 1 and 3 and with O-6 and O-8 in 2 and 4.

Synthesis of analogues of 3-deoxy-D-manno-octulosonic acid (KDO) as potential inhibitors of CMP-KDO synthetase.

A series of derivatives of the 2-deoxy analogue of beta-KDO (2,6-anhydro-3-deoxy-D-glycero-D-talo-octonic acid; ammonium salt, 2) has been synthesised as potential inhibitors of CMP-KDO synthetase, starting from methyl 2,6-anhydro-3-deoxy-4,5:7,8-di-O-isopropylidene-D-glycero-D-talo- octonate and replacing the CO2Me group attached to C-2 variously by CONH2, CONHOH, CH2OH, CH2PO(OH)(O-NH4+), COCH2PO(OH)(O-H3N+pheny), CH2CO2-NH4+, CON-HCH2CO2-NH4+, CONHBn, CONHHexyl, CO2Bn, and CO2Hexyl. Of these derivatives, the hydroxamic acid (CONHOH) was the best inhibitor of CMP-KDO synthetase, but was less potent than 2.

A 2-deoxy analogue of KDO as the first inhibitor of the enzyme CMP-KDO synthetase.

The two KDO analogues 2,6-anhydro-3-deoxy-D-glycero-D-galacto-octonate and 2,6-anhydro-3-deoxy-D-glycero-D-talo-octonate were synthesized and tested as inhibitors of the enzyme CTP:CMP-deoxyoctulosonate cytidylyltransferase (CMP-KDO synthetase) from Gram-negative bacteria. Only compound 4, the 2-deoxy analogue of beta-KDO-pyranose, was found to be an inhibitor with a Ki of 3.9 microM.