Structure-activity relationships for 1-phenylbenzimidazoles as selective ATP site inhibitors of the platelet-derived growth factor receptor

Synthesis of benzimidazole/triphenylamine-based compounds, evaluation of their bioactivities and an in silico study with receptor tyrosine kinases

The antiproliferative activity of AL-1 against various cancer cells indicated the applicability of the BI-TPA-based compound as a potential multi-cancer inhibitor.

A post-synthetically modified metal–organic framework for copper catalyzed denitrative C–N coupling of nitroarenes under heterogeneous conditions

Post-synthesis modification of DMOF, afforded a desired material for strategic infusion of catalytically active centers in a porous matrix. The catalyst is capable for denitrative C–N coupling reactions of nitroarenes under heterogeneous conditions.

Lerisetron Analogues with Antimalarial Properties: Synthesis, Structure-Activity Relationship Studies, and Biological Assessment

A phenotypic whole cell high-throughput screen against the asexual blood and liver stages of the malaria parasite identified a benzimidazole chemical series. Among the hits were the antiemetic benzimidazole drug Lerisetron 1 (IC₅₀ NF54 = 0.81 μM) and its methyl-substituted analogue 2 (IC₅₀ NF54 = 0.098 μM). A medicinal chemistry hit to lead effort led to the identification of chloro-substituted analogue 3 with high potency against the drug-sensitive NF54 (IC₅₀ NF54 = 0.062 μM) and multidrug-resistant K1 (IC₅₀ K1 = 0.054 μM) strains of the human malaria parasite Plasmodium falciparum. Compounds 2 and 3 gratifyingly showed in vivo efficacy in both Plasmodium berghei and P. falciparum mouse models of malaria. Cardiotoxicity risk as expressed in strong inhibition of the human ether-a-go-go-related gene (hERG) potassium channel was identified as a major liability to address. This led to the synthesis and biological assessment of around 60 analogues from which several compounds with improved antiplasmodial potency, relative to the lead compound 3, were identified.

A rhodamine-based fast and selective fluorescent probe for monitoring exogenous and endogenous nitric oxide in live cells

A sensitive and selective fluorescent probe for fast detection of nitric oxide was synthesized by grafting a NO-trapper o-phenylenediamine onto a rhodamine fluorophore.

Quinoxaline-Based Scaffolds Targeting Tyrosine Kinases and Their Potential Anticancer Activity

Quinoxaline derivatives, also called benzopyrazines, are an important class of heterocyclic compounds. Quinoxalines have drawn great attention due to their wide spectrum of biological activities. They are considered as an important basis for anticancer drugs due to their potential activity as protein kinase inhibitors. In this review, we focus on the chemistry of the quinoxaline derivatives, the strategies for their synthesis, their potential activities against various tyrosine kinases, and on the structure-activity relationship studies reported to date.

6-Methoxy-2-methyl-1-m-tolyl-1H-benzimidazole hemihydrate

The title compound, C₁₆H₁₆N₂O·0.5H₂O, is a substituted 1-phenyl­benzimidazole, which belongs to the class of ATP-site inhibitors of the platelet-derived growth-factor receptor. In the crystal, the components are linked by an O—H⋯N hydrogen bond.

Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds

Development of kinase-targeted therapies for central nervous system (CNS) diseases is a great challenge. Glycogen synthase kinase 3 (GSK-3) offers a great potential for severe CNS unmet diseases, being one of the inhibitors on clinical trials for different tauopathies. Following our hypothesis based on the enhanced reactivity of residue Cys199 in the binding site of GSK-3, we examine here the suitability of phenylhalomethylketones as irreversible inhibitors. Our data confirm that the halomethylketone unit is essential for the inhibitory activity. Moreover, addition of the halomethylketone moiety to reversible inhibitors turned them into irreversible inhibitors with IC(50) values in the nanomolar range. Overall, the results point out that these compounds might be useful pharmacological tools to explore physiological and pathological processes related to signaling pathways regulated by GSK-3 opening new avenues for the discovery of novel GSK-3 inhibitors.

Radial Basis Function Network-Based Transform for a Nonlinear Support Vector Machine as Optimized by a Particle Swarm Optimization Algorithm with Application to QSAR Studies

The support vector machine (SVM) has been receiving increasing interest in an area of QSAR study for its ability in function approximation and remarkable generalization performance. However, selection of support vectors and intensive optimization of kernel width of a nonlinear SVM are inclined to get trapped into local optima, leading to an increased risk of underfitting or overfitting. To overcome these problems, a new nonlinear SVM algorithm is proposed using adaptive kernel transform based on a radial basis function network (RBFN) as optimized by particle swarm optimization (PSO). The new algorithm incorporates a nonlinear transform of the original variables to feature space via a RBFN with one input and one hidden layer. Such a transform intrinsically yields a kernel transform of the original variables. A synergetic optimization of all parameters including kernel centers and kernel widths as well as SVM model coefficients using PSO enables the determination of a flexible kernel transform according to the performance of the total model. The implementation of PSO demonstrates a relatively high efficiency in convergence to a desired optimum. Applications of the proposed algorithm to QSAR studies of binding affinity of HIV-1 reverse transcriptase inhibitors and activity of 1-phenylbenzimidazoles reveal that the new algorithm provides superior performance to the backpropagation neural network and a conventional nonlinear SVM, indicating that this algorithm holds great promise in nonlinear SVM learning.

Potent platelet-derived growth factor-beta receptor (PDGF-betaR) inhibitors: Synthesis and structure-activity relationships of 7-[3-(cyclohexylmethyl)ureido]-3-{1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl}quinoxalin-2(1H)-one derivatives

We found previously that 7-[3-(cyclohexylmethyl)ureido]-3-{1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl}quinoxalin-2(1H)-one (7d-6) has considerable potency as a PDGF inhibitor. This compound showed potent inhibitory activity in a PDGF-induced CPA (Cell Proliferation Assay) and APA (Auto-Phosphorylation Assay) (IC50 = 0.05 micromol/l in CPA, 0.03 micromol/l in APA). Therefore, we tried to develop a novel and effective PDGF-betaR inhibitor by optimizing a series of its derivatives. We found that trifluoroacetic acid (TFA)-catalyzed coupling of pyrrolo[2,3-b]pyridines with quinoxalin-2-ones proceeded efficiently under mild oxidation condition with manganese(IV) oxide (MnO2) in situ, so this method was applied to prepare a series of derivatives. Results of in vitro screening of newly synthesized derivatives identified compound 7d-9 as having potent (IC50 = 0.014 micromol/l in CPA, 0.007 micromol/l in APA) and selective [IC50 values against vascular endothelial growth factor receptor 2 (VEGFR2, kinase domain region, KDR), epidermal growth factor receptor (EGFR), c-Met (hepatocyte growth factor receptor) and insulin growth factor I receptor (IGF-IR)/IC50 against PDGFR were each >1000] inhibitory activity. Moreover, in this series of derivatives, 7b-2 showed potent inhibitory activity toward both PDGF- and VEGF-induced signaling (PDGFR: IC50 = 0.004 micromol/l in CPA, 0.0008 micromol/l in APA, KDR: IC50 = 0.008 micromol/l in APA). Herein we report a new and convenient synthetic method for this series of derivatives and its SAR study.

QSAR studies on 1-phenylbenzimidazoles as inhibitors of the platelet-derived growth factor

This work is devoted to the development of quantitative structure-activity relationship (QSAR) models of the biological activity of 123 1-phenylbenzimidazoles as inhibitors of the PDGF receptor. The molecular features are represented by chemical descriptors that have been calculated on geometrical, topological, quantum mechanical, and electronic basis by using CODESSA PRO. The obtained models, linear (multilinear regression) and nonlinear (artificial neural network), are aimed to link the structures to their reported activity log 1/IC50. The former model can be used for physico-chemical interpretation, while the latter possesses a superior predictive ability.

PDGF receptor kinase inhibitors for the treatment of PDGF driven diseases

PDGF and its receptors are involved in a variety of diseases: cancers, atherosclerosis, balloon injury induced restenosis, pulmonary fibrosis and more. In all cases enhanced signaling of the receptor is the hallmark. In some cases, like chronic monomyelocytic leukemia (CMML), the persistent PDGFR signaling is essential for the survival of the cancer cell. These findings induced the research community as well as the pharmaceutical industry to develop agents that block PDGFR signaling. The possible utilization of PDGFR kinase inhibitors as anti-restenosis agents is likely to move ahead of the utilization of these agents to treat human malignancies.

Kinases, Homology Models, and High Throughput Docking

With the many protein sequences coming from the genome sequencing projects, it is unlikely that we will ever have an atomic resolution structure of every relevant protein. With high throughput crystallography, however, we will soon have representative structures for the vast majority of protein families. Thus the drug discovery and design process will rely heavily on protein modeling to address issues such as designing combinatorial libraries for an entire class of targets and engineering genome-wide selectivity over a target class. In this study we assess the value of high throughput docking into homology models. To do this we dock a database of random compounds seeded with known inhibitors into homology models of six different kinases. In five of the six cases the known inhibitors were found to be enriched by factors of 4-5 in the top 5% of the overall scored and ranked compounds. Furthermore, in the same five cases the known inhibitors were found to be enriched by factors of 2-3 in the top 5% of the scored and ranked known kinase inhibitors, thus showing that the homology models can pick up some of the crucial selectivity information.

Quantitative structure–activity relationships (QSAR): studies of inhibitors of tyrosine kinase

A quantitative structure-activity relationship (QSAR) study of the 1-phenylbenzimidazoles as inhibitors of the platelet-derived growth factor receptor (PDGFR) was performed. Some new electronic parameters Q(o), Q(m) and Q(p) are suggested for characterizing the effect of substituents. Many other descriptors are also used which are selected by evolution algorithm (EA) using modified Cp as objective function proposed by the present authors. The descriptor Q(m) is shown to be an important variable to express effect of substituents. The variable selection shows that spatial descriptors are most important variables revealing important properties of the inhibitors. Electron-releasing substitutes at 5-position and the absence of bulky groups at 4,7-positions of the parent structure can enhance inhibitor activity. Principal component analysis is performed to classify this series of compounds.

Design and synthesis of 1,5-diarylbenzimidazoles as inhibitors of the VEGF-receptor KDR

1,5-Diarylbenzimidazoles have been identified as potent inhibitors of KDR kinase activity. The series was developed with a goal of finding compounds with optimal drug-like properties. This communication describes structural modifications in the series that enhance solubility, lower protein binding, and provide compounds with excellent potency and pharmacokinetic profiles.

Stent-induced restenosis in the swine coronary artery is inhibited by a platelet-derived growth factor receptor tyrosine kinase inhibitor, TKI963

Activities of vascular smooth muscle cells (SMCs) such as proliferation, migration, and matrix production contribute to restenosis following clinical interventions of angioplasty and stent placement. Because activation of platelet-derived growth factor (PDGF)-receptor tyrosine kinase (PDGFr-TK) influences these processes and promotes restenosis, TKI963, an inhibitor of the PDGFr-TK was discovered, and its efficacy was evaluated in blocking stent-induced restenosis as analyzed by intravascular ultrasound (IVUS). TKI963, a low-molecular-weight compound, inhibited the cell-free PDGFbetar-TK with a K(i) value of 56 +/- 14 nM. TKI963 also inhibited PDGF-dependent events in human aortic SMCs (e.g., in situ PDGFr autophosphorylation, mitogenesis, chemotaxis, and collagen production with median inhibitory concentration values of approximately 300 nM) without affecting the activity of a series of membrane receptor tyrosine kinases and intracellular serine/threonine kinases. In vivo, stent-induced restenosis in the swine coronary artery was reduced by oral administration of TKI963 (1.25, 2.5, and 5 mg/kg BID, for 28 days). Late lumen cross-sectional area (CSA) loss, plaque CSA growth, and plaque volume in the stent determined by IVUS were dose-relatedly decreased (33-62% at 1.25 mg/kg BID to 66-92% at 5 mg/kg BID, depending on the parameter) compared with controls. TKI963 treatment of </=1 week following stent placement had no effect on the prevention of restenosis. TKI963, a selective, orally bioavailable inhibitor of the PDGFr-TK, dose-relatedly reduced stent-induced restenosis and did so by inhibiting PDGF-dependent activities that occur as late events following stent placement.

A single amino acid exchange inverts susceptibility of related receptor tyrosine kinases for the ATP site inhibitor STI-571

The tyrosine kinase inhibitor STI-571 potently blocks BCR-Abl, platelet-derived growth factor (PDGF) alpha- and beta-receptors, and c-Kit kinase activity. Flt3, a receptor tyrosine kinase closely related to PDGF receptors and c-Kit is, however, not inhibited by STI-571. Sequence alignments of different kinases and indications from the crystal structure of the STI-571 Abl kinase complex revealed amino acid residues that are probably crucial for this activity profile. It was predicted that Flt3 Phe-691 in the beta5 strand may sterically prevent interaction with STI-571. The point mutants Flt3 F691T and PDGFbeta-receptor T681F were constructed, and kinase assays showed that the Flt3 mutant but not the PDGFbeta-receptor mutant is inhibited by STI-571. Docking of STI-571 into computer models of the PDGFbeta-receptor and Flt3 kinase domains and comparison with the crystal structure of the STI-571 Abl kinase complex indicated very similar binding sites among the three nonphosphorylated kinases, suggesting corresponding courses of their Asp-Phe-Gly motifs and activation loops. Accordingly, we observed reduced sensitivity of preactivated compared with nonactivated PDGFR-beta for the inhibition by STI-571. Courses of the activation loop that collide with STI-571 binding explain its inactivity at other kinases as the insulin receptor. The binding site models of PDGFR-beta and Flt3 were applied to predict structural approaches for more selective PDGFbeta-receptor inhibitors.

New efficient route for solid-phase synthesis of benzimidazole derivatives

A simple and efficient method for the solid-phase synthesis of benzimidazole libraries is described. Monoalkylation of various o-phenylenediamines on resin-bound bromoacetamide proceeded smoothly to give the monoalkyl resin-bound o-phenylenediamines in high yields. Subsequent cyclization of the diamines with various aldehydes afforded solid-supported benzimidazoles. Cleavage from the resin gave benzimidazoles in good yields. The present method enabled the introduction of the diversity on the benzene ring of imidazoles. Azabenzimidazoles, such as 4-azabenzimidazoles, 5-azabenzimidazoles, and purines, were also synthesized in good yields with high purities by the same procedure.

Soluble 2-substituted aminopyrido[2,3-d]pyrimidin-7-yl ureas. Structure-activity relationships against selected tyrosine kinases and exploration of in vitro and in vivo anticancer activity

In continuing our search for medicinal agents to treat proliferative diseases, we have discovered 2-substituted aminopyrido[2,3-d]pyrimidin-7-yl ureas as a novel class of soluble, potent, broadly active tyrosine kinase (TK) inhibitors. An efficient route was developed that enabled the synthesis of a wide variety of analogues with substitution on several positions of the template. From the lead structure 1, several series of analogues were made that examined the C-6 aryl substituent, a variety of water solublizing substitutents at the C-2 position, and urea or other acyl functionality at the N-7 position. Compounds of this series were competitive with ATP and displayed submicromolar to low nanomolar potency against a panel of TKs, including receptor (platelet-derived growth factor, PDGFr; fibroblast growth factor, FGFr;) and nonreceptor (c-Src) classes. Several of the most potent compounds displayed submicromolar inhibition of PDGF-mediated receptor autophosphorylation in rat aortic vascular smooth muscle cells and low micromolar inhibition of cellular growth in five human tumor cell lines. One of the more thoroughly evaluated members, 32, with IC50 values of 0.21 microM (PDGFr), 0.049 microM (bFGFr), and 0.018 microM (c-Src), was evaluated in in vivo studies against a panel of five human tumor xenografts, with known and/or inferred dependence on the EGFr, PDGFr, and c-Src TKs. Compound 32 produced a tumor growth delay of 14 days against the Colo-205 colon xenograft model.

Structure-activity relationships for 5-substituted 1-phenylbenzimidazoles as selective inhibitors of the platelet-derived growth factor receptor

Following an earlier discovery of 1-phenylbenzimidazoles as ATP-site inhibitors of the platelet-derived growth factor receptor (PDGFR), further structure-activity relationships for analogues (particularly 5-substituted derivatives) are reported. The data are consistent with a binding model (constructed from the homology-modeled structure of the catalytic subunit of the PDGFR using protein kinase A as the template) in which the ligand binds in the relatively narrow ATP site, with the phenyl ring pointing toward the interior of the pocket and the 5-position of the benzimidazole ring toward the mouth of the pocket. The narrow binding pocket allows a maximum torsion angle between the phenyl and benzimidazole rings of about 40 degrees, consistent with that calculated (43.6 degrees) for the minimum-energy conformation of the unsubstituted free ligand. The inactivity of 7- or 2'-substituted analogues is consistent with the greater torsion angle (and thus larger ligand cross-section) of such substituted analogues. There is substantial bulk tolerance for 5-substituents, which protrude out of the mouth of the hydrophobic pocket, with the most effective analogues being those bearing weak bases. On the basis of this model, 5-OR derivatives bearing cationic side chains were prepared as soluble analogues, and these showed sub-micromolar potencies against the isolated PDGFR enzyme. They were also moderately effective inhibitors of autophosphorylation of PDGFR in rat aortic vascular smooth muscle cells, with IC50s in the range 0.1-1 microM.