The design and preliminary structure-activity relationship studies of benzotriazines as potent inhibitors of Abl and Abl-T315I enzymes

Navigating pharmacophore space to identify activity discontinuities: A case study with BCR-ABL

The exploration of chemical space is a fundamental aspect of chemoinformatics, particularly when one explores a large compound data set to relate chemical structures with molecular properties. In this study, we extend our previous work on chemical space visualization at the pharmacophoric level. Instead of using conventional binary classification of affinity (active vs inactive), we introduce a refined approach that categorizes compounds into four distinct classes based on their activity levels: super active, very active, active, and inactive. This classification enriches the color scheme applied to pharmacophore space, where the color representation of a pharmacophore hypothesis is driven by the associated compounds. Using the BCR-ABL tyrosine kinase as a case study, we identified intriguing regions corresponding to pharmacophore activity discontinuities, providing valuable insights for structure-activity relationships analysis.

3-Substituted Blatter Radicals: Cyclization of N-Arylguanidines and N-Arylamidines to Benzo[e][1,2,4]triazines and PhLi Addition

A series of 3-amino- and 3-alkyl-substituted 1-phenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yls was prepared in four steps involving N-arylation, cyclization of N-arylguanidines and N-arylamidines, reduction of the resulting N-oxides to benzo[e][1,2,4]triazines, and subsequent addition of PhLi followed by aerial oxidation. The resulting seven C(3)-substituted benzo[e][1,2,4]triazin-4-yls were analyzed by spectroscopic and electrochemical methods augmented with density functional theory (DFT) methods. Electrochemical data were compared to DFT results and correlated with substituent parameters.

An overview on the recent developments of 1,2,4-triazine derivatives as anticancer compounds

The synthesis, the antitumor activity, the SAR and, whenever described, the possible mode of action of 1,2,4-triazine derivatives, their N-oxides, N,N'-dioxides as well as the benzo- and hetero-fused systems are reported. Herein are treated derivatives disclosed to literature from the beginning of this century up to 2016. Among the three possible triazine isomers, 1,2,4-triazines are the most studied ones and many derivatives having remarkable antitumor activity have been reported in the literature and also patented reaching advanced phases of clinical trials.

Hybrid pyrimidine alkynyls inhibit the clinically resistance related Bcr-Abl(T315I) mutant

A series of pyrimidine alkynyl derivatives were designed and synthesized as new Bcr-Abl inhibitors by hybriding the structural moieties from GNF-7, ponatinib and nilotinib. One of the most potent compounds 4e strongly suppresses Bcr-Abl(WT) and Bcr-Abl(T315I) kinase with IC50 values of 5.0 and 9.0 nM, and inhibits the proliferation of K562 and murine Ba/F3 cells ectopically expressing Bcr-Abl(T315I) cells with IC50 values of 2 and 50 nM, respectively. It also displays good pharmacokinetics properties with an oral bioavailability of 35.3% and T(1/2) value of 48.7 h, and demonstrates significantly suppression on tumor growth in xenografted mice of K562 and Ba/F3 cells expressing Bcr-Abl(T315I). These inhibitors may serve as lead compounds for further developing new anticancer drugs overcoming the clinically acquired resistance against current Bcr-Abl inhibitors.

Identification of GZD824 as an orally bioavailable inhibitor that targets phosphorylated and nonphosphorylated breakpoint cluster region-Abelson (Bcr-Abl) kinase and overcomes clinically acquired mutation-induced resistance against imatinib

Bcr-Abl(T315I) mutation-induced imatinib resistance remains a major challenge for clinical management of chronic myelogenous leukemia (CML). Herein, we report GZD824 (10a) as a novel orally bioavailable inhibitor against a broad spectrum of Bcr-Abl mutants including T315I. It tightly bound to Bcr-Abl(WT) and Bcr-Abl(T315I) with K(d) values of 0.32 and 0.71 nM, respectively, and strongly inhibited the kinase functions with nanomolar IC(50) values. The compound potently suppressed proliferation of Bcr-Abl-positive K562 and Ku812 human CML cells with IC(50) values of 0.2 and 0.13 nM, respectively. It also displayed good oral bioavailability (48.7%), a reasonable half-life (10.6 h), and promising in vivo antitumor efficacy. It induced tumor regression in mouse xenograft tumor models driven by Bcr-Abl(WT) or the mutants and significantly improved the survival of mice bearing an allograft leukemia model with Ba/F3 cells harboring Bcr-Abl(T315I). GZD824 represents a promising lead candidate for development of Bcr-Abl inhibitors to overcome acquired imatinib resistance.

Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening

Although the constitutively activated break-point cluster region-Abelson (BCR-ABL) tyrosine kinase was well known to be responsible for chronic myelogenous leukemia (CML), the existence of drug-resistant mutants of BCR-ABL has made it difficult to develop effective anti-CML drugs. Here, we report the first example for a successful application of the structure-based virtual screening to identify two common inhibitors equipotent for the wild type and the most drug-resistant T315I mutant of BCR-ABL. Because both inhibitors were screened for having desirable physicochemical properties as a drug candidate and revealed micromolar inhibitory activities, they deserve consideration for further development by structure-activity relationship (SAR) studies to optimize the anti-CML activity. We also address the structural features relevant to the stabilizations of the identified inhibitors in the ATP-binding sites. The results indicate that the inhibitors should be less stabilized by the hydrogen-bond interactions with the change of the receptor from the wild type to T315I mutant due to the replacement of the hydroxy group with the ethyl moiety in the ATP-binding site. Nonetheless, the inhibitors are found to be capable of maintaining the potency for the mutant through the strengthening of hydrophobic interactions to the extent sufficient to compensate for the loss of some hydrogen bonds. This differential binding mode may serve as key information for designing new common inhibitors of the wild type and T315I mutant of BCR-ABL.

Virtual screening of Abl inhibitors from large compound libraries by support vector machines

Abl promotes cancers by regulating cell morphogenesis, motility, growth, and survival. Successes of several marketed and clinical trial Abl inhibitors against leukemia and other cancers and appearances of reduced efficacies and drug resistances have led to significant interest in and efforts for developing new Abl inhibitors. In silico methods of pharmacophore, fragment, and molecular docking have been used in some of these efforts. It is desirable to explore other in silico methods capable of searching large compound libraries at high yields and reduced false-hit rates. We evaluated support vector machines (SVM) as a virtual screening tool for searching Abl inhibitors from large compound libraries. SVM trained and tested by 708 inhibitors and 65,494 putative noninhibitors correctly identified 84.4 to 92.3% inhibitors and 99.96 to 99.99% noninhibitors in 5-fold cross validation studies. SVM trained by 708 pre-2008 inhibitors and 65 494 putative noninhibitors correctly identified 50.5% of the 91 inhibitors reported since 2008 and predicted as inhibitors 29,072 (0.21%) of 13.56M PubChem, 659 (0.39%) of 168K MDDR, and 330 (5.0%) of 6638 MDDR compounds similar to the known inhibitors. SVM showed comparable yields and substantially reduced false-hit rates against two similarity based and another machine learning VS methods based on the same training and testing data sets and molecular descriptors. These suggest that SVM is capable of searching Abl inhibitors from large compound libraries at low false-hit rates.