Design, Synthesis, and Biological Activity of 5,10-Dihydro-dibenzo[b,e][1,4]diazepin-11-one-Based Potent and Selective Chk-1 Inhibitors

Design, synthesis and evaluation of novel thienopyridazine derivatives as Chk1/2 inhibitors

In order to search for novel checkpoint kinase 1/2 (Chk1) inhibitors, we have designed and synthesized a series of new compounds incorporating thienopyridazine core. Bioevaluation showed that compounds 10j, 10i, 13e and 10o exhibited relatively good inhibitory activity. Notably, compound 10o displayed high selectivity against a panel of kinases and inhibited Chk1/2 signaling pathway stimulated by DNA damage drugs in cellular level. Molecular docking of 10o to the ATP-binding site of Chk1 kinase domain indicated the existence of polar interactions between 10o and the ATP-ribose-binding residues of Chk1. In mouse HT-29 xenografts, a synergistic effect was observed. Co-treatment by CPT-11 and 10o significantly diminished the tumor volume, indicating the great potential of 10o as a candidate of Chk1/2 inhibitor.

Synthesis and evaluation of antitumor activity of dibenzodiazepine derivatives

A series of dibenzodiazepine 2-position derivatives, bearing N-methylpiperazine at the C-11 position, were prepared by using a concise approach. Their inhibitory activities of tumor cell proliferation in vitro were tested in five cell lines, including breast cancer cell BCAP37, gastric cancer cell SGC7901, liver cancer cell HepG2, cervical cancer cell HeLa and acute promyelocytic leukemia cell HL-60. Several compounds showed efficient tumor activity with IC₅₀ values down to 0.30 μM. These compounds are expected to be a new class of potential anticancer lead compounds.

Discovery and Optimization of Dibenzodiazepinones as Allosteric Mutant-Selective EGFR Inhibitors

Allosteric kinase inhibitors represent a promising new therapeutic strategy for targeting kinases harboring oncogenic driver mutations in cancers. Here, we report the discovery, optimization, and structural characterization of allosteric mutant-selective EGFR inhibitors comprising a 5,10-dihydro-11H-dibenzo[b,e][1,4]diazepin-11-one scaffold. Our structure-based medicinal chemistry effort yielded an inhibitor (3) of the EGFR(L858R/T790M) and EGFR(L858R/T790M/C797S) mutants with an IC₅₀ of ∼10 nM and high selectivity, as assessed by kinome profiling. Further efforts to develop allosteric dibenzodiazepinone inhibitors may serve as the basis for new therapeutic options for targeting drug-resistant EGFR mutations.

Palladium-catalysed regioselective N-arylation of anthranilamides: a tandem route for dibenzodiazepinone synthesis

A palladium-catalyzed tandem reaction of 2-aminobenzamide and 1,2-dihaloarenes for the synthesis of dibenzodiazepinone via double N-arylations (inter and intra-molecular) has been achieved.

Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods

Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.

Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor

The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strategy of a dibenzodiazepine hit 1, discovered in a fragment-based screen, yielding highly potent and selective inhibitors of PAK1 such as 2 and 3. Compound 2 was cocrystallized with PAK1 to confirm binding to an allosteric site and to reveal novel key interactions. Compound 3 modulated PAK1 at the cellular level and due to its selectivity enabled valuable research to interrogate biological functions of the PAK1 kinase.

Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment

X-ray-based alignments of bioactive compounds are commonly used to correlate structural changes with changes in potencies, ultimately leading to three-dimensional quantitative structure-activity relationships such as CoMFA or CoMSIA models that can provide further guidance for the design of new compounds. We have analyzed data sets where the alignment of the compounds is entirely based on experimentally derived ligand poses from X-ray-crystallography. We developed CoMFA and CoMSIA models from these X-ray-determined receptor-bound conformations and compared the results with models generated from ligand-centric Template CoMFA, finding that the fluctuations in the positions and conformations of compounds dominate X-ray-based alignments can yield poorer predictions than those from the self-consistent template CoMFA alignments. Also, when there exist multiple different binding modes, structural interpretation in terms of binding site constraints can often be simpler with template-based alignments than with X-ray-based alignments.

Concise copper-catalyzed synthesis of tricyclic biaryl ether-linked aza-heterocyclic ring systems

A new method for the synthesis of tricyclic biaryl ether-linked ring systems incorporating seven-, eight-, and nine-membered ring amines is presented. In the presence of catalytic quantities of copper(I), readily accessible acyclic precursors undergo an intramolecular carbon-oxygen bond-forming reaction facilitated by a "templating" chelating nitrogen atom. The methodology displays a broad substrate scope, is practical, and generates rare and biologically interesting tricyclic heteroaromatic products that are difficult to access by other means.

The N-aryl aminocarbonyl ortho-substituent effect in Cu-catalyzed aryl amination and its application in the synthesis of 5-substituted 11-oxo-dibenzodiazepines

Double amination of ortho-substituted aryl bromides proceeded under mild conditions to afford 5-substituted 11-oxo-dibenzodiazepines, which revealed that there is a strong ortho-substituent effect caused by N-aryl aminocarbonyl groups during copper-catalyzed aryl amination.

Therapeutic implications for the induced levels of Chk1 in Myc-expressing cancer cells

PURPOSE

The transcription factor c-Myc (or "Myc") is a master regulator of pathways driving cell growth and proliferation. MYC is deregulated in many human cancers, making its downstream target genes attractive candidates for drug development. We report the unexpected finding that B-cell lymphomas from mice and patients exhibit a striking correlation between high levels of Myc and checkpoint kinase 1 (Chk1).

EXPERIMENTAL DESIGN

By in vitro cell biology studies as well as preclinical studies using a genetically engineered mouse model, we evaluated the role of Chk1 in Myc-overexpressing cells.

RESULTS

We show that Myc indirectly induces Chek1 transcript and protein expression, independently of DNA damage response proteins such as ATM and p53. Importantly, we show that inhibition of Chk1, by either RNA interference or a novel highly selective small molecule inhibitor, results in caspase-dependent apoptosis that affects Myc-overexpressing cells in both in vitro and in vivo mouse models of B-cell lymphoma.

CONCLUSION

Our data suggest that Chk1 inhibitors should be further evaluated as potential drugs against Myc-driven malignancies such as certain B-cell lymphoma/leukemia, neuroblastoma, and some breast and lung cancers.

Concise palladium-catalyzed synthesis of dibenzodiazepines and structural analogues

A general and highly efficient protocol for the synthesis of dibenzodiazepines and their structural analogues is reported. In the presence of catalytic quantities of palladium, readily accessible precursors are cross-coupled with ammonia and then spontaneously undergo an intramolecular condensation to form the corresponding dibenzodiazepines in one step. This new strategy is applicable to the construction of a wide variety of dibenzooxazepines and other structurally related heterocycles.

Application of Ullmann and Ullmann-Finkelstein reactions for the synthesis of N-aryl-N-(1H-pyrazol-3-yl) acetamide or N-(1-aryl-1H-pyrazol-3-yl) acetamide derivatives and pharmacological evaluation

Ullmann-type reactions are becoming a major tool in medicinal chemistry. In this article, we describe the use of these Copper-catalyzed reactions with various precursors, acyl-heteroarylamines or pyrazoles of interest for pharmacomodulation. To the medicinal chemist they offer new, usually untapped disconnection approaches to compounds of interest. They thus open the way to new original analogues of bioactive compounds possibly not patented, from common building-blocks. They also allow C to N bioisosteric replacements, which sometimes are synthetically challenging. We report for the first time the critical effect of acetylamino substituents on the regioselective arylation of unsymmetrical pyrazoles that are useful for medicinal chemists. Finally, we have applied this strategy to the design of novel AT(1) receptor antagonists. Though this family has been extensively investigated in the past 30 years, N-arylation and C to N replacement made possible by Ullmann chemistry, can produce original antagonists.

Identification of inhibitors of checkpoint kinase 1 through template screening

Checkpoint kinase 1 (CHK1) is an oncology target of significant current interest. Inhibition of CHK1 abrogates DNA damage-induced cell cycle checkpoints and sensitizes p53 deficient cancer cells to genotoxic therapies. Using template screening, a fragment-based approach to small molecule hit generation, we have identified multiple CHK1 inhibitor scaffolds suitable for further optimization. The sequential combination of in silico low molecular weight template selection, a high concentration biochemical assay and hit validation through protein-ligand X-ray crystallography provided 13 template hits from an initial in silico screening library of ca. 15000 compounds. The use of appropriate counter-screening to rule out nonspecific aggregation by test compounds was essential for optimum performance of the high concentration bioassay. One low molecular weight, weakly active purine template hit was progressed by iterative structure-based design to give submicromolar pyrazolopyridines with good ligand efficiency and appropriate CHK1-mediated cellular activity in HT29 colon cancer cells.

Pharmacophore modeling and virtual screening studies of checkpoint kinase 1 inhibitors

In this study, chemical feature-based 3-dimensional (3D) pharmacophore models of Checkpoint kinase 1 (Chk1) inhibitors were developed based on the known inhibitors of Chk1. The best pharmacophore model Hypo1 was characterized by the best correlation coefficient (0.9577), and the lowest root mean square deviation (0.8871). Hypo1 consists of one hydrogen-bond acceptor, one hydrogen-bond donor, and two hydrophobic features, as well as one excluded volume. This pharmacophore model was further validated by both test set and cross validation methods. A comparison analysis of Hypo1 with chemical features in the active site of Chk1 indicates that the pharmacophore model Hypo1 can correctly reflect the interactions between Chk1 and its ligands. Then Hypo1 was used to screen chemical databases, including Specs and Chinese Nature Product Database (CNPD) for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking study to refine the retrieved hits. Finally some of the most potent (estimated) compounds were selected from the final refined hits and suggested for further experimental investigation.

Investigation of novel 7,8-disubstituted-5,10-dihydro-dibenzo[b,e][1,4]diazepin-11-ones as potent Chk1 inhibitors

The synthesis and structure-activity relationships (SAR) of Chk1 inhibitors based on a 5,10-dihydro-dibenzo[b,e][1,4]diazepin-11-one core are described. Specifically, an exploration of the 7 and 8 positions on this previously disclosed core afforded compounds with improved enzymatic and cellular potency.