alpha,alpha-Cyclopentaneglycine dipeptides capped with biaryls as tachykinin NK(2) receptor antagonists.

The NK(2) receptor belongs to the family of tachykinin neurotransmitters. It has been reported to be involved in several pathological conditions, and selective antagonists are potentially useful drugs for the treatment of asthma, irritable bowel syndrome, cystitis, and depression. Starting from in-house capped dipeptide libraries, we were able to identify a number of molecules with sub-nanomolar binding affinity for the hNK(2) receptor. All were characterized by a rigid core structure with a strong constraint induced by an alpha,alpha-cyclopentaneglycine fragment. Herein we report the further elaboration of three initial basic structures. The planar benzothiophene group was substituted with a series of biphenyl and heterobiphenyl moieties that are well tolerated in terms of receptor affinity. The new compounds also maintained good antagonist potency in an in vitro functional assay, and a number of them showed significant in vivo activity after intravenous administration in our guinea pig model.

Synthesis, biological evaluation, and molecular modeling studies of rebeccamycin analogues modified in the carbohydrate moiety.

A new series of indolocarbazole glycosides containing disaccharides were synthesized and their in vitro antiproliferative activity was evaluated against three human cancer cell lines (A2780, H460, and GLC4). Cytotoxicity appeared to be remarkably affected by the regio- and stereochemical features of the disaccharide moiety. In vivo antitumor activity of the compounds studied, two of which having IC(50)<100 nm, was determined using ovarian cancer cell line A2780 xenografted on nude mice. One compound showed an efficacy similar to that of the reference compound edotecarin, though with a lower long-lasting activity. The topoisomerase I inhibitory properties of some compounds were also examined. Molecular dynamics simulations of the ternary topoisomerase I-DNA-ligand complexes were performed to analyze the structural features of topoisomerase I poisoning with this class of indolocarbazoles. A plausible explanation of their biological behavior was provided. These theoretical results were compared with the recently published crystal structure of an indolocarbazole monosaccharide bound to the covalent human topoisomerase I-DNA complex.

Caco-2 cell permeability modelling: a neural network coupled genetic algorithm approach.

The ability to cross the intestinal cell membrane is a fundamental prerequisite of a drug compound. However, the experimental measurement of such an important property is a costly and highly time consuming step of the drug development process because it is necessary to synthesize the compound first. Therefore, in silico modelling of intestinal absorption, which can be carried out at very early stages of drug design, is an appealing alternative procedure which is based mainly on multivariate statistical analysis such as partial least squares (PLS) and neural networks (NN). Our implementation of neural network models for the prediction of intestinal absorption is based on the correlation of Caco-2 cell apparent permeability (P (app)) values, as a measure of intestinal absorption, to the structures of two different data sets of drug candidates. Several molecular descriptors of the compounds were calculated and the optimal subsets were selected using a genetic algorithm; therefore, the method was indicated as Genetic Algorithm-Neural Network (GA-NN). A methodology combining a genetic algorithm search with neural network analysis applied to the modelling of Caco-2 P (app) has never been presented before, although the two procedures have been already employed separately. Moreover, we provide new Caco-2 cell permeability measurements for more than two hundred compounds. Interestingly, the selected descriptors show to possess physico-chemical connotations which are in excellent accordance with the well known relevant molecular properties involved in the cellular membrane permeation phenomenon: hydrophilicity, hydrogen bonding propensity, hydrophobicity and molecular size. The predictive ability of the models, although rather good for a preliminary study, is somewhat affected by the poor precision of the experimental Caco-2 measurements. Finally, the generalization ability of one model was checked on an external test set not derived from the data sets used to build the models. The result obtained is of interesting practical application and underlines that the successful model construction is strictly dependent on the structural space representation of the data set used for model development.

Generation of a new class of hNK(2) receptor ligands using the 'fragment approach'.

The so called 'fragment approach' was applied in the search for new leads as selective hNK(2) antagonists. A first round of structural space exploration through the use of bond rigidity as scaffold to support the fragments, afforded 27a as 200 nM hNK(2) ligand. Further refinement gave MEN 14933 as a 16 nM hNK(2) ligand, selective versus hNK(1), of a novel class. Conformational analysis was used to study results and plan future work.

An unusual rearrangement of Zofenopril, a new ACE inhibitor drug: mass spectrometric and conformational studies.

Zofenopril (1) is a new ACE inhibitor, used in therapy for hypertension and post-myocardial infarction. The protonated quasi-molecular ion (m/z 430) of 1, obtained under positive electrospray ionization conditions, loses a benzoic acid molecule (m/z 308), which in turn decomposes via loss of CO (m/z 280) when low-energy collisional-induced dissociation (CID) and in-source experiments are performed. This rearrangement is the main fragmentation process and can be observed both in-source and in the product ion tandem mass spectra, using either an ion trap or a triple quadrupole instrument. Other known diastereoisomers of 1, an impurity with an acetyl in the place of the benzoyl group (2) and an impurity with two propanoyl chains in series (3), give the same rearrangement. On the other hand, the mass spectra of the methyl ester (4) and an impurity with two proline moieties (5) do not show this unusual fragmentation. Time-resolved CID spectra of 1 show that the rearrangement occurs after about 2 ms, a time scale comparable to those of the other non-rearrangement cleavages. These experiments suggest a conformation in the gas phase for 1 in which the benzoyl group is close to the hydroxyl of the carboxylic acid group, from which the rearrangement could readily occur. Since compounds 4 and 5 do not show the same behaviour, the presence of a carboxylic acid in the proline ring seems to play a crucial role in the rearrangement, probably due to an intramolecular hydrogen bond. To confirm this hypothesis, deuterium exchanges in mass spectrometric experiments and a conformational analysis via computational methods were performed.