Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs

Synthesis, anti-inflammatory activity, and in vitro antitumor effect of a novel class of cyclooxygenase inhibitors: 4-(aryloyl)phenyl methyl sulfones

Following our previous research on anti-inflammatory drugs (NSAIDs), we report on the design and synthesis of 4-(aryloyl)phenyl methyl sulfones. These substances were characterized for their capacity to inhibit cyclooxygenase (COX-1 and COX-2) isoenzymes. Molecular modeling studies showed that the methylsulfone group of these compounds was inserted deep in the pocket of the human COX-2 binding site, in an orientation that precludes hydrogen bonding with Arg120, Ser353, and Tyr355 through their oxygen atoms. The N-arylindole 33 was the most potent inhibitor of COX-2 and also the most selective (COX-1/COX-2 IC(50) ratio was 262). The indole derivative 33 was further tested in vivo for its anti-inflammatory activity in rats. This compound showed greater inhibitory activity than ibuprofen. Other compounds (20, 26, 9, and 30) showed strong activity against carrageenan-induced inflammation. The latter compounds showed a weak capacity to inhibit the proliferation of human cell lines K562, NCI-H460, and HT-29 in vitro.

MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Abeta(10-35)) aggregation

Recent experiments with amyloid-beta (Aβ) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer’s disease. The toxicity of Aβ oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Aβ₁₀₋₃₅ monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

Fever

Measurement of body temperature remains one of the most common ways to assess health. An increase in temperature above what is considered to be a normal value is inevitably regarded as a sure sign of disease and referred to with one simple word: fever. In this review, we summarize how research on fever allowed the identification of the exogenous and endogenous molecules and pathways mediating the fever response. We also show how temperature elevation is common to different pathologies and how the molecular components of the fever-generation pathway represent drug targets for antipyretics, such as acetylsalicylic acid, the first "blockbuster drug". We also show how fever research provided new insights into temperature and energy homeostasis, and into treatment of infection and inflammation.

Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities

In this article, the concept of multi conformation-based quantitative structure-activity relationship (MCB-QSAR) is proposed, and based upon that, we describe a new approach called the side-chain conformational space analysis (SCSA) to model and predict protein-peptide binding affinities. In SCSA, multi-conformations (rather than traditional single-conformation) have received much attention, and the statistical average information on multi-conformations of side chains is determined using self-consistent mean field theory based upon side chain rotamer library. Thereby, enthalpy contributions (including electrostatic, steric, hydrophobic interaction and hydrogen bond) and conformational entropy effects to the binding are investigated in terms of occurrence probability of residue rotamers. Then, SCSA was applied into the dataset of 419 HLA-A 0201 binding peptides, and nonbonding contributions of each position in peptide ligands are well determined. For the peptides, the hydrogen bond and electrostatic interactions of the two ends are essential to the binding specificity, van der Waals and hydrophobic interactions of all the positions ensure strong binding affinity, and the loss of conformational entropy at anchor positions partially counteracts other favorable nonbonding effects.

A ligand's-eye view of protein binding

Docking tools created for structure-based design and virtual screening have also been used to automate ligand alignment for comparative molecular field analysis (CoMFA). Models based on such alignments have been compared with those obtained based solely on shared ligand substructures, but such comparisons have generally failed to distinguish between conformational specification (alignment in the internal coordinate space) and embedding in a shared external frame of reference (Cartesian alignment). Here, large sets of inhibitors were docked into two cyclooxygenase and two reverse transcriptase crystal structures, and the poses generated were evaluated in terms of the CoMFA models they produced. Realigning the conformers obtained by docking by rigid-body rotation and translation to overlay their common substructures improved model statistics and interpretability, provided the protein structure used for docking was reasonably appropriate to the ligands being considered.

Ligand Coordinate Analysis of SC-558 from the Active Site to the Surface of COX-2: A Molecular Dynamics Study

We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published crystal structure of COX-2 with SC-558 in the active site (1cx2) was taken, and the ligand was moved incrementally in 13 steps. At each of these points on the path, exhaustive minimization and dynamics calculations were performed. The role of water was found to be important in these computations. An average structure was obtained from 250 conformations at each point and minimized. At each point on the path, the 10 lowest-energy conformations were also selected; a consideration of the average and lowest conformations provides fine details on the consistency of specific and strong interactions, and also on the geometry of the ligand. The movement of the ligand through the protein may be divided into three stages that are distinguished from each other because of energy and geometry discontinuities in both the ligand and the protein. The first of these covers the region between the active site and the point at 5.8 A from it. The second, which covers the distance between 8.2 and 10.0 A and is associated with maximum energetic and structural instability, is of critical importance. The third stage covers the distance between 10.5 A and the exterior and represents a stage of increasing hydration and expulsion of the ligand from the protein. Our results provide a confirmation for the existence of a shallow cavity near the protein surface in which the ligand is bound reversibly. By examining the residues that show maximum mobility, one obtains an idea of the gating mechanism that governs the entry and exit of the protein into or from the deep pocket that contains the active site. We note, however, that the variation of the root-mean-square deviation of all residues begins to increase almost as soon as the ligand leaves the active site, and even before there are any changes in the gate inter-residue distances. This loosening of the protein even before the gate opens might be a part of the enthalpy-entropy balance that accompanies the ligand's passage through the protein. Our results provide an energy profile of the ligand during its entry/exit into/from the protein and can, in principle, enable one to assess the residence time, which in turn may be associated or indirectly correlated with adverse cardiovascular side effects of nonsteroidal anti-inflammatory drugs. We believe that similar analyses for other selected COX-2-specific inhibitors will provide a measure (or prediction) of possible toxicity effects.

Antitumor properties of dimethyl-celecoxib, a derivative of celecoxib that does not inhibit cyclooxygenase-2: implications for glioma therapy

✓ Celecoxib (Celebrex) appears to be unique among the class of selective COX-2 inhibitors (coxibs), because this particular compound exerts a second function that is independent of its celebrated ability to inhibit COX-2. This second function is the potential to inhibit cell proliferation and stimulate apoptotic cell death at much lower concentrations than any other coxibs. Intriguingly, these two functions are mediated by different moieties of the celecoxib molecule and can be separated. The author, as well as others, have generated and investigated analogs of celecoxib that retain only one of these two functions. One derivative, 2,5-dimethyl-celecoxib (DMC), which retains the antiproliferative and apoptosis-inducing function, but completely lacks the COX-2 inhibitory activity, is able to mimic faithfully all of the numerous antitumor effects of celecoxib that have been investigated so far, including reduction of neovascularization and inhibition of experimental tumor growth in various in vivo tumor models. In view of the controversy that has recently arisen regarding the life-threatening side effects of this class of coxibs, it may be worthwhile to pursue further the potential benefits of drugs such as DMC for anticancer therapy. Because DMC is not a coxib yet potently maintains celecoxib's antitumor potential, one may be inclined to speculate that this novel compound could potentially be advantageous in the management of COX-2–independent cancers. In this summary, the implications of recent findings with DMC will be presented and discussed.

Influence of plasma protein on the potencies of inhibitors of cyclooxygenase-1 and -2

It is widely believed that the potencies of nonsteroid anti-inflammatory drugs (NSAIDs) as inhibitors of cyclooxygenase (COX) are influenced by protein binding in the extracellular fluid, since NSAIDs are bound to circulating albumin by well over 95%. This is an important point because the protein concentrations in synovial fluid and the central nervous system, which are sites of NSAID action, are markedly different from those in plasma. Here we have used a modified whole-blood assay to compare the potencies of aspirin, celecoxib, diclofenac, indomethacin, lumiracoxib, meloxicam, naproxen, rofecoxib, sodium salicylate, and SC560 as inhibitors of COX-1 and COX-2 in the presence of differing concentrations of protein. The potencies of diclofenac, naproxen, rofecoxib, and salicylate, but not aspirin, celecoxib, indomethacin, lumiracoxib, meloxicam, or SC560, against COX-1 (human platelets) increased as protein concentrations were reduced. Varying protein concentrations did not affect the potencies of any of the drugs against COX-2, with the exception of sodium salicylate (A549 cells). Clearly, our findings show that the selectivity of inhibitors for COX-1 and COX-2, which are taken to be linked to their efficacy and side effects, may change in different extracellular fluid conditions. In particular, selectivity in one body compartment does not demonstrate selectivity in another. Thus, whole-body safety or toxicity cannot be linked to one definitive measure of COX selectivity.

Inhibition of cytokine-induced prostanoid biogenesis by phytochemicals in human colonic fibroblasts

Many of the inflammatory pathways regulating the production of prostanoids are implicated in the development of colon cancer. Diets rich in fruits and vegetables are associated with decreased rates of colon cancer and this may reflect anti-inflammatory properties of some phytochemicals in plant-based foods. In order to ascertain which of the many dietary compounds may be protective, a cell-based screening method was established to determine their effects on the production of prostanoids. By up-regulating prostaglandin H synthase-2 in human colonic fibroblast cells with cytokines, we have investigated the potential protective effect of a structurally related group of phytochemicals on prostanoid biogenesis. Several of the compounds significantly inhibited prostanoid biogenesis, by up to 81% and others enhanced prostanoid production. All of the compounds that enhanced prostanoid production belonged to the hydroxylated benzoic acid family and good correlation was observed with their redox activity and the ability to enhance prostanoid production. Common structural features of the inhibitors were the presence of 4-hydroxyl and 3-methoxyl substituents on the aromatic ring and/or the presence of a three-carbon side-chain on C1.

TOPS-MODE based QSARs derived from heterogeneous series of compounds. Applications to the design of new anti-inflammatory compounds

A new application of TOPological Sub-structural MOlecular DEsign (TOPS-MODE) was carried out in anti-inflammatory compounds using computer-aided molecular design. Two series of compounds, one containing anti-inflammatory and the other containing nonanti-inflammatory compounds were processed by a k-means cluster analysis in order to design the training and prediction sets. A linear classification function to discriminate the anti-inflammatory from the inactive compounds was developed. The model correctly and clearly classified 88% of active and 91% of inactive compounds in the training set. More specifically, the model showed a good global classification of 90%, that is, (399 cases out of 441). While in the prediction set, they showed an overall predictability of 88% and 84% for active and inactive compounds, being the global percentage of good classification of 85%. Furthermore this paper describes a fragment analysis in order to determine the contribution of several fragments towards anti-inflammatory property, also the present of halogens in the selected fragments were analyzed. It seems that the present TOPS-MODE based QSAR is the first alternate general 'in silico' technique to experimentation in anti-inflammatory discovery.

Computational studies of COX-2 inhibitors: 3D-QSAR and docking

The 3D-QSAR (three-dimensional quantitative structure-activity relationships) studies for 88 selective COX-2 (cyclooxygenase-2) inhibitors belonging to three chemical classes (triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides) were conducted using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Partial least squares analysis produced statistically significant models with q(2) values of 0.84 and 0.79 for CoMFA and CoMSIA, respectively. The binding energies calculated from flexible docking were correlated with inhibitory activities by the least-squares fit method. The three chemical classes of inhibitors showed reasonable internal predictability (r(2)=0.51, 0.49, and 0.54), but the sulfonyl-containing inhibitors demonstrated distinctively low binding energy compared to the others. The electrostatic interaction energy between the Arg513 of the COX-2 active site and sulfonyl group of the triaryl rings seemed to have the responsibility for difference in binding energy. Comparative binding energy (COMBINE) analyses gave q(2) values of 0.64, 0.63, and 0.50 for triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides, respectively. In this COMBINE model, some protein residues were highlighted as particularly important for inhibitory activity. The combination of ligand-based and structure-based models provided an improved understanding in the interaction between the three chemical classes and the COX-2.