Identification of [4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)-2-pyrimidinyl] amines and ethers as potent and selective cyclooxygenase-2 inhibitors

Radiotracers for Imaging of Inflammatory Biomarkers TSPO and COX-2 in the Brain and in the Periphery

Inflammation involves the activation of innate immune cells and is believed to play an important role in the development and progression of both infectious and non-infectious diseases such as neurodegeneration, autoimmune diseases, pulmonary and cancer. Inflammation in the brain is marked by the upregulation of translocator protein (TSPO) in microglia. High TSPO levels are also found, for example, in macrophages in cases of rheumatoid arthritis and in malignant tumor cells compared to their relatively low physiological expression. The same applies for cyclooxgenase-2 (COX-2), which is constitutively expressed in the kidney, brain, thymus and gastrointestinal tract, but induced in microglia, macrophages and synoviocytes during inflammation. This puts TSPO and COX-2 in the spotlight as important targets for the diagnosis of inflammation. Imaging modalities, such as positron emission tomography and single-photon emission tomography, can be used to localize inflammatory processes and to track their progression over time. They could also enable the monitoring of the efficacy of therapy and predict its outcome. This review focuses on the current development of PET and SPECT tracers, not only for the detection of neuroinflammation, but also for emerging diagnostic measures in infectious and other non-infectious diseases such as rheumatic arthritis, cancer, cardiac inflammation and in lung diseases.

Design, synthesis and antitumor activity evaluation of trifluoromethyl-substituted pyrimidine derivatives

In order to find efficient new antitumor drugs, a series of novel trifluoromethyl-substituted pyrimidine derivatives were designed and synthesized, and the bioactivity against four human tumor cells (PC-3, MGC-803, MCF-7 and H1975) was evaluated by MTT assay. Compound 17v displayed potent anti-proliferative activity on H1975 (IC₅₀=2.27 μΜ), which was better than the positive control 5-FU (IC₅₀=9.37 μΜ). Further biological evaluation studies showed that compound 17v induced apoptosis of H1975 cells and arrested the cell cycle at G2/M phase. Furthermore, compound 17v induced H1975 cells apoptosis through increasing the expression of pro-apoptotic proteins Bax and p53 and down-regulating the anti-apoptotic protein Bcl-2. In addition, compound 17v was able to be tightly embedded in the active pocket of EGFR. In summary, these results demonstrated that compound 17v has a potential as a lead compound for further investigation.

Identification of Potential COX-2 Inhibitors for the Treatment of Inflammatory Diseases Using Molecular Modeling Approaches

Non-steroidal anti-inflammatory drugs are inhibitors of cyclooxygenase-2 (COX-2) that were developed in order to avoid the side effects of non-selective inhibitors of COX-1. Thus, the present study aims to identify new selective chemical entities for the COX-2 enzyme via molecular modeling approaches. The best pharmacophore model was used to identify compounds within the ZINC database. The molecular properties were determined and selected with Pearson’s correlation for the construction of quantitative structure–activity relationship (QSAR) models to predict the biological activities of the compounds obtained with virtual screening. The pharmacokinetic/toxicological profiles of the compounds were determined, as well as the binding modes through molecular docking compared to commercial compounds (rofecoxib and celecoxib). The QSAR analysis showed a fit with R = 0.9617, R² = 0.9250, standard error of estimate (SEE) = 0.2238, and F = 46.2739, with the tetra-parametric regression model. After the analysis, only three promising inhibitors were selected, Z-964, Z-627, and Z-814, with their predicted pIC₅₀ (−log IC₅₀) values, Z-814 = 7.9484, Z-627 = 9.3458, and Z-964 = 9.5272. All candidates inhibitors complied with Lipinski’s rule of five, which predicts a good oral availability and can be used in in vitro and in vivo tests in the zebrafish model in order to confirm the obtained in silico data.

Classification of Cyclooxygenase-2 Inhibitors Using Support Vector Machine and Random Forest Methods

This work reports the classification study conducted on the biggest COX-2 inhibitor data set so far. Using 2925 diverse COX-2 inhibitors collected from 168 pieces of literature, we applied machine learning methods, support vector machine (SVM) and random forest (RF), to develop 12 classification models. The best SVM and RF models resulted in MCC values of 0.73 and 0.72, respectively. The 2925 COX-2 inhibitors were reduced to a data set of 1630 molecules by removing intermediately active inhibitors, and 12 new classification models were constructed, yielding MCC values above 0.72. The best MCC value of the external test set was predicted to be 0.68 by the RF model using ECFP_4 fingerprints. Moreover, the 2925 COX-2 inhibitors were clustered into eight subsets, and the structural features of each subset were investigated. We identified substructures important for activity including halogen, carboxyl, sulfonamide, and methanesulfonyl groups, as well as the aromatic nitrogen atoms. The models developed in this study could serve as useful tools for compound screening prior to lab tests.

Rational Use of Heterogeneous Data in Quantitative Structure-Activity Relationship (QSAR) Modeling of Cyclooxygenase/Lipoxygenase Inhibitors

Numerous studies have been published in recent years with acceptable quantitative structure-activity relationship (QSAR) modeling based on heterogeneous data. In many cases, the training sets for QSAR modeling were constructed from compounds tested by different biological assays, contradicting the opinion that QSAR modeling should be based on the data measured by a single protocol. We attempted to develop approaches that help to determine how heterogeneous data should be used for the creation of QSAR models on the basis of different sets of compounds tested by different experimental methods for the same target and the same endpoint. To this end, more than 100 QSAR models for the IC50 values of ligands interacting with cyclooxygenase 1,2 (COX) and seed lipoxygenase (LOX), obtained from ChEMBL database were created using the GUSAR software. The QSAR models were tested on the external set, including 26 new thiazolidinone derivatives, which were experimentally tested for COX-1,2/LOX inhibition. The IC50 values of the derivatives varied from 89 μM to 26 μM for LOX, from 200 μM to 0.018 μM for COX-1, and from 210 μM to 1 μM for COX-2. This study showed that the accuracy of the models is dependent on the distribution of IC50 values of low activity compounds in the training sets. In the most cases, QSAR models created based on the combined training sets had advantages in comparison with QSAR models, based on a single publication. We introduced a new method of combination of quantitative data from different experimental studies based on the data of reference compounds, which was called "scaling".

Pyrimidine-based fluorescent COX-2 inhibitors: synthesis and biological evaluation

The cyclooxygenase-2 (COX-2) enzyme is overexpressed in a variety of cancers and mediates inflammatory processes that aid the growth and progression of malignancies. Three novel and selective fluorescent COX-2 inhibitors have been designed and synthesized on the basis of previously reported pyrimidine-based COX-2 inhibitors and the 7-nitrobenzofurazan fluorophore. In vitro evaluation of COX-1/COX-2 isozyme inhibition identified N-(2-((7-nitro-benzo[c][1,2,5]oxadiazol-4-yl)amino)propyl)-4-[4-(methylsulfonyl)phenyl]-6-(trifluoro-methyl)-pyrimidin-2-amine (6) as a novel potent and selective COX-2 inhibitor (IC50 = 1.8 μM). Lead compound (6) was further evaluated for its ability to selectively visualize COX-2 isozyme in COX-2 expressing human colon cancer cell line HCA-7 using confocal microscopy experiments.

SAR and QSAR models of cyclooxygenase-1 (COX-1) inhibitors

Cyclooxygenase-1 (COX-1) is one isoform of COX, and it is a main target of nonsteroidal anti-inflammatory drugs (NSAIDs). It is important to develop efficient and selective COX-1 inhibitors. In this work, 12 classification models for 1530 cyclooxygenase-1 (COX-1) inhibitors were built by support vector machine (SVM), decision tree (DT) and random forest (RF) methods. The best classification model (model 1A) was built by SVM with MACCS fingerprints. The classification accuracies for the training and test sets were 99.67% and 97.39%, respectively. The Matthews correlation coefficient (MCC) of the test set was 0.94. We also divided the 1530 COX-1 inhibitors into nine subsets according to their different scaffolds using Kohonen's self-organizing map (SOM). In addition, six quantitative structure-activity relationship (QSAR) models for 181 COX-1 inhibitors whose IC₅₀ were measured by enzyme immunoassay were built by multiple linear regression (MLR) and SVM. The best QSAR model (model 5A) was built by SVM with CORINA Symphony descriptors. The correlation coefficients of the training and test sets are 0.93 and 0.84, respectively. The models built in this study can be obtained from the authors.

Impact of structural alterations on the radiopharmacological profile of 18F-labeled pyrimidines as cyclooxygenase-2 (COX-2) imaging agents

INTRODUCTION

Non-invasive imaging of COX-2 in cancer represents a powerful tool for assessing COX-2-mediated effects on chemoprevention and radiosensitization using potent and selective COX-2 inhibitors as an emerging class of anticancer drugs. Careful assessment of the pharmacokinetic profile of radiolabeled COX-2 inhibitors is of crucial importance for the development of suitable radiotracers for COX-2 imaging in vivo. The delicate balance between the selection of typical COX-2 pharmacophores and the resulting physicochemical characteristics of the COX-2 inhibitor represents a formidable challenge for the search of radiolabeled COX-2 imaging agents. Several pyrimidine-based COX-2 inhibitors demonstrated favorable in vitro and in vivo COX-2 imaging properties in various COX-2 expressing cancer cell lines. Here, we describe a comparative radiopharmacological study of three ¹⁸F-labeled COX-2 inhibitors based on a pyrimidine scaffold. The objective of this study was to investigate how subtle structural alterations influence the pharmacokinetic profile of lead compound [¹⁸F]1a ([¹⁸F]Pyricoxib) to afford ¹⁸F-labeled pyrimidine-based COX-2 inhibitors with improved COX-2 imaging properties in vivo.

METHODS

Radiosynthesis of radiotracers was accomplished through reaction with 4-[¹⁸F]fluorobenzyl amine on a methyl-sulfone labeling precursor ([¹⁸F]1a and [¹⁸F]2a) or late-stage radiofluorination using a iodyl-containing labeling precursor ([¹⁸F]3a). Radiopharmacological profile of ¹⁸F-labeled pyrimidine-based COX-2 inhibitors [¹⁸F]1a, [¹⁸F]2a and [¹⁸F]3a was studied in COX-2-expressing human HCA-7 colorectal cancer cell line, including cellular uptake studies in HCA-7 cells and dynamic PET imaging studies in HCA-7 xenografts.

RESULTS

Cellular uptake of radiotracers [¹⁸F]2a and [¹⁸F]3a in HCA-7 cells was 450% and 300% radioactivity/mg protein, respectively, after 90 min incubation, compared to 600% radioactivity/mg protein for radiotracer [¹⁸F]1a. Dynamic PET imaging studies revealed a tumor SUV of 0.53 ([¹⁸F]2a) and 0.54 ([¹⁸F]3a) after 60 min p.i. with a tumor-to-muscle ratio of ~1. Tumor SUV for [¹⁸F]1a (60 min p.i.) was 0.76 and a tumor-to-muscle ratio of ~1.5. Pyricoxib analogues [¹⁸F]2a and [¹⁸F]3a showed distinct pharmacokinetic profiles in comparison to lead compound [¹⁸F]1a with a significantly improved lung clearance pattern. Replacing the 4-[¹⁸F]fluorobenzyl amine motif in radiotracer [¹⁸F]1a with a 4-[¹⁸F]fluorobenzyl alcohol motif in radiotracer [¹⁸F]3a resulted in re-routing of the metabolic pathway as demonstrated by a more rapid liver clearance and higher initial kidney uptake and more rapid kidney clearance compared to radiotracers [¹⁸F]1a and [¹⁸F]2a. Moreover, radiotracer [¹⁸F]3a displayed favorable rapid brain uptake and retention.

CONCLUSION

The radiopharmacological profile of three ¹⁸F-labeled COX-2 inhibitors based on a pyrimidine scaffold were evaluated in COX-2 expressing human colorectal cancer cell line HCA-7 and HCA-7 xenografts in mice. Despite the overall structural similarity and comparable COX-2 inhibitory potency of all three radiotracers, subtle structural alterations led to significantly different in vitro and in vivo metabolic profiles.

ADVANCES IN KNOWLEDGE

Among all tested pyrimidine-based ¹⁸F-labeled COX-2 inhibitors, lead compound [¹⁸F]1a remains the most suitable radiotracer for assessing COX-2 expression in vivo. Radiotracer [¹⁸F]3a showed significantly improved first pass pulmonary passage in comparison to radiotracer [¹⁸F]1a and might represents a promising lead compound for the development of radiotracers for PET imaging of COX-2 in neuroinflammation.

Synthesis, Fungicidal Activity and Mode of Action of 4-Phenyl-6-trifluoromethyl-2-aminopyrimidines against Botrytis cinerea

Anilinopyrimidines are the main chemical agents for management of Botrytis cinerea. However, the drug resistance in fungi against this kind of compounds is very serious. To explore new potential fungicides against B. cinerea, a series of 4-phenyl-6-trifluoromethyl-2-amino-pyrimidine compounds (compounds III-1 to III-22) were synthesized, and their structures were confirmed by ¹H-NMR, IR and MS. Most of these compounds possessed excellent fungicidal activity. The compounds III-3 and III-13 showed higher fungicidal activity than the positive control pyrimethanil on fructose gelatin agar (FGA), and compound III-3 on potato dextrose agar (PDA) indicated high activity compared to the positive control cyprodinil. In vivo greenhouse results indicated that the activity of compounds III-3, III-8, and III-11 was significantly higher than that of the fungicide pyrimethanil. Scanning electron micrography (SEM) and transmission electron micrography (TEM) were applied to illustrate the mechanism of title compounds against B. cinerea. The title compounds, especially those containing a fluorine atom at the ortho-position on the benzene ring, could maintain the antifungal activity against B. cinerea, but their mechanism of action is different from that of cyprodinil. The present study lays a good foundation for us to find more efficient reagents against B. cinerea.

Cyclooxygenase-2 inhibitors: a literature and patent review (2009 - 2010)

INTRODUCTION

COXs catalyze the complex conversion of arachidonic acid to prostaglandins and thromboxanes, which trigger as autacoids with autocrine and paracrine biological effects many physiological and pathophysiological responses. The structural similarities of the COX-1 and -2 enzymes make the search for selective inhibitors for COX-2 versus -1 a formidable challenge.

AREAS COVERED

The present review provides a survey of the development of novel COX-2 inhibitors covering literature and patents between 2009 and 2010. The presence of a central, typically 1,2-diaryl substituted, heterocycle or carbocycle as a characteristic structural motif in many selective COX-2 inhibitors represents the basis of their classification in this review. The classification in this review includes COX-2 inhibitors based on five- and six-membered heterocycles, benzoheterocycles (e.g., benzopyrans, benzopyranones, indoles and quinolines), quinones, chalcones, natural products and miscellaneous. When available, COX-2 inhibitors are presented with their related COX-2 inhibitory potency and selectivity.

EXPERT OPINION

The availability of detailed information on the crystal structure of the COX-2 enzyme with various substrates, cofactors and inhibitors, and the recently reported increased risk of cardiovascular events associated with selective COX-2 inhibitors will further stimulate development of COX-2 inhibitors with favorable COX-2 inhibition profiles without adverse effects to the cardiovascular system.

Pyrimidine derivatives as potent and selective A3 adenosine receptor antagonists

Two regioisomeric series of diaryl 2- or 4-amidopyrimidines have been synthesized and their adenosine receptor affinities were determined in radioligand binding assays at the four human adenosine receptors (hARs). Some of the ligands prepared herein exhibit remarkable affinities (K(i) < 10 nm) and, most noticeably, the absence of activity at the A(1), A(2A), and A(2B) receptors. The structural determinants that support the affinity and selectivity profiles of the series were highlighted through an integrated computational approach, combining a 3D-QSAR model built on the second generation of GRid INdependent Descriptors (GRIND2) with a novel homology model of the hA(3) receptor. The robustness of the computational model was subsequently evaluated by the design of new derivatives exploring the alkyl substituent of the exocyclic amide group. The synthesis and evaluation of the novel compounds validated the predictive power of the model, exhibiting excellent agreement between predicted and experimental activities.

Nonsteroidal Anti-Inflammatory Drugs (NSAIDs): Progress in Small Molecule Drug Development

Ever since the discovery of aspirin, small molecule therapeutics have been widely prescribed to treat inflammation and pain. Aspirin and several small molecule NSAIDs are known to inhibit the enzymes cyclooxygenase-1 (COX-1) and -2 (COX-2). Despite the success of NSAIDs to treat inflammatory disorders, the development of a clinically useful small molecule NSAIDs with decreased side effect profiles is an ongoing effort. The recent discovery and development of selective COX-2 inhibitors was a step toward this direction. Emerging trends are represented by the progress in the development of hybrid agents such as nitric oxide donor-NSAIDs (NO-NSAIDs) and dual COX/lipoxygenase (LOX) inhibitors. This review focuses on the recent advances in the rational design of small molecule NSAIDs in therapy.