Oriol Llorens

Differential binding mode of diverse cyclooxygenase inhibitors

Non-steroidal anti-inflammatory drugs (NSAIDs) are competitive inhibitors of cyclooxygenase (COX), the enzyme that mediates biosynthesis of prostaglandins and thromboxanes from arachidonic acid. There are at least two different isoforms of the enzyme known as COX-1 and -2. Site directed mutagenesis studies suggest that non-selective COX inhibitors of diverse chemical families exhibit differential binding modes to the two isozymes. These results cannot clearly be explained from the sole analysis of the crystal structures of COX available from X-ray diffraction studies. With the aim to elucidate the structural features governing the differential inhibitory binding behavior of these inhibitors, molecular modeling studies were undertaken to generate atomic models compatible with the experimental data available. Accordingly, docking of different COX inhibitors, including selective and non-selective ligands: rofecoxib, ketoprofen, suprofen, carprofen, zomepirac, indomethacin, diclofenac and meclofenamic acid were undertaken using the AMBER program. The results of the present study provide new insights into a better understanding of the differential binding mode of diverse families of COX inhibitors, and are expected to contribute to the design of new selective compounds.

Structural basis of the dynamic mechanism of ligand binding to cyclooxygenase.

Molecular modeling studies performed on the two cyclooxygenase (COX) isozymes suggest that the cavity at the mouth of the active site on the membrane domain that may act as an actual binding site of COX ligands. Actual docking of different inhibitors at this site provides a structural basis to explain the dynamics of COX inhibition.

Synthesis and biological evaluation of 1,3,4-triaryl-3-pyrrolin-2-ones, a new class of selective cyclooxygenase-2 inhibitors.

The synthesis and structure activity relationships (SAR) of a series of novel selective COX-2 inhibitors are reported. The results show that some of the 1,3,4-triaryl-3-pyrrolin-2-ones 1 are more potent as COX-2 inhibitors than celecoxib, and that lactam Id has the same selectivity.

Molecular Modeling in the Design of Peptidomimetics and Peptide Surrogates

The most important natural sources of new leads are plant extracts, bacterial broths, animal venoms and peptides isolated from living organisms. However, only the three first have been used extensively in the development of new therapeutic agents. This is probably due to the low pharmacological profile exhibited by peptides, that requires a lengthy transformation to make them suitable as new leads. In contrast, bioactive compounds isolated from the other sources are regularly closer to be used as lead compounds. Nevertheless, the sources for compounds of this category are nowadays scarce. In contrast, there are new bioactive peptides discovered quite often and reported as ligands for different receptors. Under these circumstances peptides appear as an attractive source of prospective new leads. In order to reduce the time involved in the design of a potential lead from a peptide, molecular modeling tools have been developed in the last few years. The purpose of the present work is to review the different techniques available and to report various successful examples of design of new peptidomimetics published in the literature.

Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies

The geometrical features of the proposed bioactive conformation of peptide T assessed by computational methods in a previous study, together with available structure-activity studies on peptide T, led us to propose a pharmacophore for the CD4-peptide T interaction. Subsequent, data base searching permitted us to identify amygdalin as a peptide T peptidomimetic.

New insights into the conformational requirements of B2 Bradykinin Antagonism

The conformational profiles of a selected group of a new series of small linear and cyclic penta- and hexapeptides, inspired on the C-terminal segment of second-generation bradykinin (BK) antagonists, were independently computed in order to assess the chemical and geometrical requirements necessary for BK antagonism. Specifically, four cyclic peptides: cyclo-(Gly-Thi-D-Tic-Oic-Arg), cyclo-(Gly-Ala-D-Tic-Oic-Arg), cyclo-(Abu-Ala-Ser-D-Tic-Oic-Arg), cyclo-(Abu-D-Phe-Ala-D-Tic-Oic-Arg), and a linear peptide: Thi-Ser-D-Tic-Oic-Arg were selected for the present study. The first three BK analogs are capable to antagonize kinin-induced rabbit jugular vein and rabbit aorta smooth muscle contraction, while last two show no detectable affinity for the BK B2 receptor. The conformational space of the five peptides was thoroughly explored using simulated annealing (SA) in an iterative fashion as sampling technique. The bioactive conformation was assessed by pairwise cross comparisons between each of the unique low energy conformations found for each of the different peptides studied within a 5 kcal/mol threshold in respect to the global minimum. The conformational profile of the highly potent BK antagonist HOE-140, computed in an independent study, was also used in conjunction with the bioactive form assessed in the present study, to propose a pharmacophore that includes the stereochemical requirements for B2 BK antagonism.

Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones

The potentiation of central cholinergic activity has beenproposed as a therapeutic approach for improving cognitivefunction in patients with Alzheimers disease. Increasingthe acetylcholine concentration in brain by modulatingacetylcholinesterase (AChE) activity is among the mostpromising strategies. We have used a combinatorial approachto identify different 2,5-piperazinediones (DKP) with AChEinhibitory activity. Our goal was to find inhibitorsexhibiting high AChE/BuChE (butyrylcholinesterase)selectivity, in order to reduce the undesirable sideeffects elicited by most of the inhibitors that have beendeveloped to date. Screening of a DKP library constructedon solid-phase using the multiple parallel synthesisformat, resulted in the identification of several compoundswith moderate efficacy on AChE. In particular, DKP-80had an IC50 = 2.2 μM with no significant inhibitoryactivity on BuChE. Moreover, estimated values of Clog P andlog BB for the most active compounds fulfilled thebioavailability requirements for enzyme inhibitors actingon the central nervous system. In order to understand theinhibitory properties of the ligand at the molecular level,molecular dynamics simulations were computed on DKP-80 complexed to AChE, and the most relevant bindinginteractions of this inhibitor to the active center of theenzyme were characterized. Overall the present resultsindicate that the DKP-based compounds identified are novelAChE inhibitors which may be considered likely leadcompounds for further development of drug candidatesagainst Alzheimers disease.

A proposed bioactive form of peptide T and the design of peptidomimetics

Peptide T is a non-natural octapeptide of sequence Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr, taken from the sequence of the protein gp 120 of HIV. The peptide has been shown to bind competitively to the CD4 receptors of the helper/inducer lymphocytes T. The peptide is presently used for the treatment of AIDS-associated dementia and has been proven useful for the treatment of psoriasis. Using molecular modeling procedures, we studied the conformational profile of this peptide as well as those of several active and inactive analogs. The analysis of these results gave rise to the proposal of a bioactive conformation of the peptide, which can be described as a pseudo β-turn structure, involving the last four residues at the C-terminus of the peptide. The secondary structure is stabilized by a hydrogen bond between the hydroxyl hydrogen of the side chain of Thr5 and the carbonyl oxygen of Tyr7. From the bioactive form and different structure-activity relationship studies, a pharmacophore was proposed. This hypothesis was used to search on several 3D data bases. One of the hits obtained was the natural compound amigdalin, which was tested and exhibited moderate activity.