Design and synthesis of 7H-pyrrolo[2,3-d]pyrimidines as focal adhesion kinase inhibitors. Part 2

Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations

Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.

Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculation Insights into the Binding Mechanism between VS-4718 and Focal Adhesion Kinase

Focal adhesion kinase (FAK) is a 125 kDa nonreceptor tyrosine kinase that plays an important role in many carcinomas. Thus, the targeting of FAK by small molecules is considered to be promising for cancer therapy. Some FAK inhibitors have been reported as potential anticancer drugs and have entered into clinical development; for example, VS-4718 is currently undergoing clinical trials. However, the lack of crystal structural data for the binding of VS-4718 with FAK has hindered the optimization of this anticancer agent. In this work, the VS-4718/FAK interaction model was obtained by molecular docking and molecular dynamics simulations. The binding free energies of VS-4718/FAK were also calculated using the molecular mechanics generalized Born surface area method. It was found that the aminopyrimidine group formed hydrogen bonds with the C502 residue of the hinge loop, while the D564 residue of the T-loop interacted with the amide group. In addition, I428, A452, V484, M499, G505, and L553 residues formed hydrophobic interactions with VS-4718. The obtained results therefore provide an improved understanding of the interaction between human FAK and VS-4718. Based on the obtained binding mechanism, 47 novel compounds were designed to target the adenosine 5'-triphosphate-binding pocket of human FAK, and ensemble docking was performed to assess the effects of these modifications on the inhibitor binding affinity. This work is also expected to provide additional insights into potential future target design strategies based on VS-4718.

Identification of Thieno[3,2-d]pyrimidine Derivatives as Dual Inhibitors of Focal Adhesion Kinase and FMS-like Tyrosine Kinase 3

Focal adhesion kinase (FAK) is overexpressed in highly invasive and metastatic cancers. To identify novel FAK inhibitors, we designed and synthesized various thieno[3,2-d]pyrimidine derivatives. An intensive structure-activity relationship (SAR) study led to the identification of 26 as a lead. Moreover, 26, a multitargeted kinase inhibitor, possesses excellent potencies against FLT3 mutants as well as FAK. Gratifyingly, 26 remarkably inhibits recalcitrant FLT3 mutants, including F691L, that cause drug resistance. Importantly, 26 is superior to PF-562271 in terms of apoptosis induction, anchorage-independent growth inhibition, and tumor burden reduction in the MDA-MB-231 xenograft mouse model. Also, 26 causes regression of tumor growth in the MV4-11 xenograft mouse model, indicating that it could be effective against acute myeloid leukemia (AML). Finally, in an orthotopic mouse model using MDA-MB-231, 26 remarkably prevents metastasis of orthotopic tumors to lymph nodes. Taken together, the results indicate that 26 possesses potential therapeutic value against highly invasive cancers and relapsed AML.

FAK inhibitors as promising anticancer targets: present and future directions

FAK, a nonreceptor tyrosine kinase, has been recognized as a novel target class for the development of targeted anticancer agents. Overexpression of FAK is a common occurrence in several solid tumors, in which the kinase has been implicated in promoting metastases. Consequently, designing and developing potent FAK inhibitors is becoming an attractive goal, and FAK inhibitors are being recognized as a promising tool in our armamentarium for treating diverse cancers. This review comprehensively summarizes the different classes of synthetically derived compounds that have been reported as potent FAK inhibitors in the last three decades. Finally, the future of FAK-targeting smart drugs that are designed to slow down the emergence of drug resistance is discussed.

Discovery of a Pyrimidothiazolodiazepinone as a Potent and Selective Focal Adhesion Kinase (FAK) Inhibitor

Focal adhesion kinase (FAK) is a tyrosine kinase with prominent roles in protein scaffolding, migration, angiogenesis, and anchorage-independent cell survival and is an attractive target for the development of cancer therapeutics. However, current FAK inhibitors display dual kinase inhibition and/or significant activity on several kinases. Although multitargeted activity is at times therapeutically advantageous, such behavior can also lead to toxicity and confound chemical-biology studies. We report a novel series of small molecules based on a tricyclic pyrimidothiazolodiazepinone core that displays both high potency and selectivity for FAK. Structure-activity relationship (SAR) studies explored modifications to the thiazole, diazepinone, and aniline "tail," which identified lead compound BJG-03-025. BJG-03-025 displays potent biochemical FAK inhibition (IC₅₀ = 20 nM), excellent kinome selectivity, activity in 3D-culture breast and gastric cancer models, and favorable pharmacokinetic properties in mice. BJG-03-025 is a valuable chemical probe for evaluation of FAK-dependent biology.

Targeting FAK in human cancer: from finding to first clinical trials

It is twenty years since Focal Adhesion Kinase (FAK) was found to be overexpressed in many types of human cancer. FAK plays an important role in adhesion, spreading, motility, invasion, metastasis, survival, angiogenesis, and recently has been found to play an important role as well in epithelial to mesenchymal transition (EMT), cancer stem cells and tumor microenvironment. FAK has kinase-dependent and kinase independent scaffolding, cytoplasmic and nuclear functions. Several years ago FAK was proposed as a potential therapeutic target; the first clinical trials were just reported, and they supported further studies of FAK as a promising therapeutic target. This review discusses the main functions of FAK in cancer, and specifically focuses on recent novel findings on the role of FAK in cancer stem cells, microenvironment, epithelial-to-mesenchymal transition, invasion, metastasis, and also highlight new approaches of targeting FAK and critically discuss challenges that lie ahead for its targeted therapeutics. The review provides a summary of translational approaches of FAK-targeted and combination therapies and outline perspectives and future directions of FAK research.

Targeting angiogenesis and the tumor microenvironment

The role of the microenvironment during the initiation and progression of malignancy is appreciated to be of critical importance for improved molecular diagnostics and therapeutics. The tumor microenvironment is the product of a crosstalk between different cells types. Active contribution of tumor-associated stromal cells to cancer progression has been recognized. Stromal elements consist of the extracellular matrix, fibroblasts of various phenotypes, and a scaffold comprised of immune and inflammatory cells, blood and lymph vessels, and nerves. This review focuses on therapeutic targets in the microenvironment related to tumor endothelium, tumor associated fibroblasts, and the extracellular matrix.

Advances in the discovery of selective JAK inhibitors

In this review, we describe the current knowledge of the biology of the JAKs. The JAK family comprises the four nonreceptor tyrosine kinases JAK1, JAK2, JAK3, and Tyk2, all key players in the signal transduction from cytokine receptors to transcription factor activation. We also review the progresses made towards the optimization of JAK inhibitors and the importance of their selectivity profile. Indeed, the full array of many medicinal chemistry enabling tools (HTS, X-ray crystallography, scaffold morphing, etc.) has been deployed to successfully design molecules that discriminate among JAK family and other kinases. While the first JAK inhibitor was launched in 2011, this review also summarizes the status of several other small-molecule JAK inhibitors currently in development to treat arthritis, psoriasis, organ rejection, and multiple cancer types.

Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route

Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the physicochemical properties of complexes of pharmaceutical interest. Even if the geometric properties of a modeled protein-ligand complex can be well predicted by computational methods, it is still challenging to rank with chemical accuracy a series of ligand analogues in a consistent way. In this article, we face this issue calculating relative binding free energies of a focal adhesion kinase, an important target for the development of anticancer drugs, with pyrrolopyrimidine-based ligands having different inhibitory power. To this aim, we employ steered molecular dynamics simulations combined with nonequilibrium work theorems for free energy calculations. This technique proves very powerful when a series of ligand analogues is considered, allowing one to tackle estimation of protein-ligand relative binding free energies in a reasonable time. In our cases, the calculated binding affinities are comparable with those recovered from experiments by exploiting the Michaelis-Menten mechanism with a competitive inhibitor.

Thioxopyrimidine in Heterocyclic Synthesis I: Synthesis of Some Novel 6-(Heteroatom-substituted)-(thio)pyrimidine Derivatives

A series of novel N-cycloalkanes, morpholine, piperazines, pyrazole, pyrimidine, benzimidazolo[1,2-a]pyrimidine, 1,2,3,4-tetrazolo[1,5-a]pyrimidine, azopyrazolo[1,5- a]pyrimidine, pyrimido[4', 5':3,4]pyrazolo[1,5-a]pyrimidines and pyridine derivatives incorporating a 5-cyano-4-methyl-2-phenyl-(thio)pyrimidine moiety were obtained by the intramolecular cyclization of 6-methylthio-pyrimidine, 6-(benzoylmethyl)thio- pyrimidine and 2-[(5-cyano-4-methyl-2-phenylpyrimidin-6-yl)thio]-3-dimethyl- amino-1-phenyl-prop-2-en-1-one with appropriate amines and enaminone compounds, respectively. The structure of all new synthesized compounds was established from their spectral data, elemental analysis and the X-ray crystal analysis.

Synthesis, Characterisation and Bioactivity of Polysubstituted 1-(4-(1H-Pyrrol-1-yl)Phenyl)-1H-Pyrrole Derivatives

1,4-Phenylenediamine reacted readily with chloroacetone to give 1,4-bis[(2-oxopropyl)amino]benzene which was used to prepare 1-(4-(1H-pyrrol-1-yl)phenyl)-1H-pyrrole derivatives in a one pot reaction with dimethylformamide dimethylacetal or triethyl orthoformate and an active methylene nitrile, an active methylene ketone or an ylidene-malononitrile. Reaction of 1,4-bis[(2-oxopropyl)amino]benzene with arene diazonium salts afforded the hydrazone derivatives which readily cyclised when reacted with malononitrile to give bispyrrole derivatives. The antibacterial activity of some of the products was determined.

Short synthesis of ethyl 3-(3-aminophenyl)propanoate

A short and effective synthesis of ethyl 3-(3-aminophenyl)propanoate is presented, employing a tandem Knoevenagel condensation/alkylidene reduction of 3-nitrobenzaldehyde with Meldrum's acid in TEAF (triethylammonium formate) followed by reduction of the intermediate 3-(3-nitrophenyl)propanoic acid by stannous chloride in ethanol. The use of stannous chloride as the reducing agent in ethanol enabled the simultaneous esterification of the carboxylic acid. Thus, stannous chloride was acting simultaneously as a Lewis acid, which activates the carboxylic acid towards a nucleophilic attack by ethanol.

Focal adhesion kinase and p53 signal transduction pathways in cancer

Human cancer is characterized by a process of tumor cell motility, invasion, and metastasis. One of the critical tyrosine kinases that is linked to these processes of tumor invasion and survival is the Focal Adhesion Kinase (FAK). Our laboratory was the first to isolate FAK from human tumors, and we had demonstrated that FAK mRNA was up-regulated in invasive and metastatic human breast and colon cancer samples. We have cloned FAK promoter and have found that FAK promoter contains p53 binding sites, and that p53 inhibits FAK transcription and regulates its expression in tumor samples. In addition, we have found a high correlation between FAK overexpression and p53 mutations in 600 population-based series of breast cancer patients. found that N-myc binds FAK promoter and induces FAK transcription in neuroblastoma cells. Thus, this review will be focused on FAK and p53 signal transduction pathways in cancer.

2-Amino-aryl-7-aryl-benzoxazoles as potent, selective and orally available JAK2 inhibitors

A series of novel benzoxazole derivatives has been designed and shown to exhibit attractive JAK2 inhibitory profiles in biochemical and cellular assays, capable of delivering compounds with favorable PK properties in rats. Synthesis and structure-activity relationship data are also provided.

Molecular-targeted therapy for cancer and nanotechnology

In order to stop malignant tumor growth, >90% of a critical biochemical pathway needs to be blocked. Due to extraordinary advances in molecular biology, there is an increased understanding of rationale and relevant molecular targets in cancer. However, due to the heterogeneity of the molecular abnormalities in multiple tumor types, strategies designed to interfere with multiple molecular abnormalities will be necessary to impact survival. Nanoparticles have the potential to provide therapies not possible with other drug modalities. Researchers and clinicians must take advantage of these opportunities in order for nanotechnology to make an impact in the diagnosis and treatment of malignancy. A discussion of relevant targets either on the cell surface or the cytoplasm and strategies to achieve optimal drug targeting are the focus of this chapter.

Astrocytic tumors

Astrocytic gliomas are the most common primary brain tumors and account for up to two thirds of all tumors of glial origin. In this review we outline the basic histological and epidemiological aspects of the different astrocytoma subtypes in adults. In addition, we summarize the key genetic alterations that have been attributed to astrocytoma patho-genesis and progression. Recent progress has been made by interpreting genetic alterations in a pathway-related context so that they can be directly targeted by the application of specific inhibitors. Also, the first steps have been taken in refining classical histopathological diagnosis by use of molecular predictive markers, for example, MGMT promoter hypermethylation in glioblastomas. Progress in this direction will be additionally accelerated by the employment of high-throughput profiling techniques, such as array-CGH and gene expression profiling. Finally, the tumor stem cell hypothesis has challenged our way of understanding astrocytoma biology by emphasizing intratumoral heterogeneity. Novel animal models will provide us with the opportunity to comprehensively study this multilayered disease and explore novel therapeutic approaches in vivo.

Highly efficient palladium-catalyzed hydrostannation of ethyl ethynyl ether

The palladium-catalyzed hydrostannation of acetylenes is widely exploited in organic synthesis as a means of forming vinyl stannanes for use in palladium-catalyzed cross-coupling reactions. Application of this methodology to ethyl ethynyl ether results in an enol ether that is challenging to isolate from the crude reaction mixture because of incompatibility with typical silica gel chromatography. Reported here is a highly efficient procedure for the palladium-catalyzed hydrostannation of ethyl ethynyl ether using 0.1% palladium(0) catalyst and 1.0 equiv of tributyltin hydride. The product obtained is a mixture of regioisomers that can be carried forward with exclusive reaction of the beta-isomer. This method is highly reproducible; relative to previously reported procedures, it is more economical and involves a more facile purification procedure.

Building skeletally diverse architectures on the Indoline Scaffold: the discovery of a chemical probe of focal adhesion kinase signaling networks

Inspired by bioactive indoline alkaloid natural products, here, we report a divergent synthesis approach that led to skeletally diverse indoline alkaloid-inspired compounds. The natural product-inspired compounds obtained were then subjected to a series of in vitro and cellular assays to examine their properties as modulators of focal adhesion kinase (FAK) activity. This study resulted in the identification of a promising lead inhibitor of FAK (42), which also showed activity in a wound healing and cell invasion assay. The in silico study of the lead compound (42) was also undertaken.

Cellular Characterization of a Novel Focal Adhesion Kinase Inhibitor

Focal adhesion kinase (FAK) is a member of a family of non-receptor protein-tyrosine kinases that regulates integrin and growth factor signaling pathways involved in cell migration, proliferation, and survival. FAK expression is increased in many cancers, including breast and prostate cancer. Here we describe perturbation of adhesion-mediated signaling with a FAK inhibitor, PF-573,228. In vitro, this compound inhibited purified recombinant catalytic fragment of FAK with an IC(50) of 4 nM. In cultured cells, PF-573,228 inhibited FAK phosphorylation on Tyr(397) with an IC(50) of 30-100 nM. Treatment of cells with concentrations of PF-573,228 that significantly decreased FAK Tyr(397) phosphorylation failed to inhibit cell growth or induce apoptosis. In contrast, treatment with PF-573,228 inhibited both chemotactic and haptotactic migration concomitant with the inhibition of focal adhesion turnover. These studies show that PF-573,228 serves as a useful tool to dissect the functions of FAK in integrin-dependent signaling pathways in normal and cancer cells and forms the basis for the generation of compounds amenable for preclinical and patient trials.

Focal adhesion kinase and p53 signaling in cancer cells

The progression of human cancer is characterized by a process of tumor cell motility, invasion, and metastasis to distant sites, requiring the cancer cells to be able to survive the apoptotic pressures of anchorage-independent conditions. One of the critical tyrosine kinases linked to these processes of tumor invasion and survival is the focal adhesion kinase (FAK). FAK was first isolated from human tumors, and FAK mRNA was found to be upregulated in invasive and metastatic human breast and colon cancer samples. Recently, the FAK promoter was cloned, and it has been found to contain p53-binding sites. p53 inhibits FAK transcription, and recent data show direct binding of FAK and p53 proteins in vitro and in vivo. The structure of FAK and p53, proteins interacting with FAK, and the role of FAK in tumorigenesis and FAK-p53-related therapy are reviewed. This review focuses on FAK signal transduction pathways, particularly on FAK and p53 signaling, revealing a new paradigm in cell biology, linking signaling from the extracellular matrix to the nucleus.

Molecular pathways triggering glioma cell invasion

The efficacy of treating malignant gliomas with adjuvant therapies remains largely unsuccessful due to the inability to effectively target invading cells. Although our understanding of glioma oncogenesis has steadily improved, the molecular mechanisms that mediate glioma invasion are still poorly understood. It is clear that genetic alterations in malignant gliomas affect cell proliferation and cell cycle control, which are the targets of most chemotherapeutic agents. However, effective therapy against cell invasion has been less successful. Future treatment protocols must incorporate pharmacotherapeutic strategies that target resistant infiltrative glioma cells as well as proliferating ones. Thus, delineating the point of convergence of signaling pathways, which mediate glioma invasion, proliferation and apoptosis, may identify novel targets that can serve as possible points of therapeutic intervention. The optimization of novel strategies will require reliable preclinical testing using an in vivo animal model of brain invasion. Current applications of existing animal models are not currently optimized or characterized for use in glioma invasion research. As such, the development of a bona fide brain invasion model in vivo must be established. Progress in understanding molecular mechanisms driving glioma invasion will be critical to the success of managing and improving the outcome of patients with this grave disease.

Integrin-regulated FAK-Src signaling in normal and cancer cells

Integrins can alter cellular behavior through the recruitment and activation of signaling proteins such as non-receptor tyrosine kinases including focal adhesion kinase (FAK) and c-Src that form a dual kinase complex. The FAK-Src complex binds to and can phosphorylate various adaptor proteins such as p130Cas and paxillin. In normal cells, multiple integrin-regulated linkages exist to activate FAK or Src. Activated FAK-Src functions to promote cell motility, cell cycle progression and cell survival. Recent studies have found that the FAK-Src complex is activated in many tumor cells and generates signals leading to tumor growth and metastasis. As both FAK and Src catalytic activities are important in promoting VEGF-associated tumor angiogenesis and protease-associated tumor metastasis, support is growing that FAK and Src may be therapeutically relevant targets in the inhibition of tumor progression.