Inhibitors of the RET tyrosine kinase based on a 2-(alkylsulfanyl)-4-(3-thienyl)nicotinonitrile scaffold

Regioselective Partial Hydrogenation and Deuteration of Tetracyclic (Hetero)aromatic Systems Using a Simple Heterogeneous Catalyst

The introduction of added '3-dimensionality' through late-stage functionalisation of extended (hetero)aromatic systems is a powerful synthetic approach. The abundance of starting materials and cross-coupling methodologies to access the precursors allows for highly diverse products. Subsequent selective partial reduction can alter the core structure in a manner of interest to medicinal chemists. Herein, we describe the precise, partial reduction of multicyclic heteroaromatic systems using a simple heterogeneous catalyst. The approach can be extended to introduce deuterium (again at late-stage). Excellent yields can be obtained using simple reaction conditions.

Identification of 3-(5-cyano-6-oxo-pyridin-2-yl)benzenesulfonamides as novel anticancer agents endowed with EGFR inhibitory activity

New 5-cyano-6-oxo-pyridine-based sulfonamides (6a-m and 8a-d) were designed and synthesized to potentially inhibit both the epidermal growth factor receptor (EGFR) and carbonic anhydrase (CA), with anticancer properties. First, the in vitro anticancer activity of each target substance was tested using Henrietta Lacks cancer cell line and M.D. anderson metastasis breast cancer cell line cells. Then, the possible CA inhibition against the human CA isoforms I, II, and IX was investigated, together with the EGFR inhibitory activity, with the most powerful derivatives. The neighboring methoxy group may have had a steric effect on the target sulfonamides, which prevented them from effectively inhibiting the CA isoforms while effectively inhibiting the EGFR. The effects of the 5-cyanopyridine derivatives 6e and 6l on cell-cycle disruption and the apoptotic potential were then investigated. To investigate the binding mechanism and stability of the target molecules, thorough molecular modeling assessments, including docking and dynamic simulation, were performed.

Design and Synthesis of Novel Thieno[3,2-c]quinoline Compounds with Antiproliferative Activity on RET-Dependent Medullary Thyroid Cancer Cells

RET kinase gain-of-function mutations represent the main cause of the high aggressiveness and invasiveness of medullary thyroid cancer (MTC). The selective inhibition of the RET kinase is a suitable strategy for the treatment of this endocrine neoplasia. Herein, we performed an innovative ligand-based virtual screening protocol using the DRUDITonline web service, focusing on the RET kinase as a biological target. In this process, thieno[3,2-c]quinolines 6a-e and 7a-e were proposed as new potential RET inhibitors. The selected compounds were synthetized by appropriate synthetic strategies, and in vitro evaluation of antiproliferative properties conducted on the particularly aggressive MTC cell line TT(C634R) identified compounds 6a-d as promising anticancer agents, with IC50 values in the micromolar range. Further structure-based computational studies revealed a significant capability of the most active compounds to the complex RET tyrosine kinase domain. The interesting antiproliferative results supported by in silico predictions suggest that these compounds may represent a starting point for the development of a new series of small heterocyclic molecules for the treatment of MTC.

Novel Set of Highly Substituted Bis-pyridines: Synthesis, Molecular Docking and Drug-Resistant Antibacterial Profile

Aims: Development of antimicrobial agents having the ability to prevent bacterial biofilm formation which causes serious health problems, especially with antibiotic-resistant bacterial strains. Materials and methods: The use of 1,3-diaryl enones as structural motifs to access the pyridine core. Antimicrobial activities of the synthesized compounds against methicillin-susceptible Staphylococcus aureus, methicillin-resistant S. aureus and vancomycin-resistant S. aureus bacterial strains were investigated. Results: The newly synthesized bis-enones were used as building blocks to access some novel highly substituted bis-pyridine derivatives. Several novel bis-compounds showed great bacterial biofilm eradication activity. Conclusion: A new series of bis-chalcones was synthesized and their structural diversity was exploited to access the corresponding, more biologically active, pyridine core. These bis-pyridines showed respectable antibacterial activities against various drug-resistant bacterial strains: namely, methicillin-susceptible, methicillin-resistant and vancomycin-resistant S. aureus.

4-Heteroaryl Substituted Amino-3,5-Dicyanopyridines as New Adenosine Receptor Ligands: Novel Insights on Structure-Activity Relationships and Perspectives

A new set of amino-3,5-dicyanopyridines was synthesized and biologically evaluated at the adenosine receptors (ARs). This chemical class is particularly versatile, as small structural modifications can influence not only affinity and selectivity, but also the pharmacological profile. Thus, in order to deepen the structure–activity relationships (SARs) of this series, different substituents were evaluated at the diverse positions on the dicyanopyridine scaffold. In general, the herein reported compounds show nanomolar binding affinity and interact better with both the human (h) A₁ and A_2A ARs than with the other subtypes. Docking studies at hAR structure were performed to rationalize the observed affinity data. Of interest are compounds 1 and 5, which can be considered as pan ligands as binding all the ARs with comparable nanomolar binding affinity (A₁AR: 1, K_i = 9.63 nM; 5, K_i = 2.50 nM; A_2AAR: 1, K_i = 21 nM; 5, Ki = 24 nM; A₃AR: 1, Ki = 52 nM; 5, Ki = 25 nM; A_2BAR: 1, EC₅₀ = 1.4 nM; 5, EC₅₀ = 1.12 nM). Moreover, these compounds showed a partial agonist profile at all the ARs. This combined AR partial agonist activity could lead us to hypothesize a potential effect in the repair process of damaged tissue that would be beneficial in both wound healing and remodeling.

Synthetic and Reactions Routes to Tetrahydrothieno[3,2-b]Quinoline Derivatives (Part IV)

Abstract:

This review describes the synthesis and chemical reactivity of tetrahydrothieno[3,2-b] quinoline derivatives from through many of the reagents such as; 1, 2-dihydropyridine-3-carbonitrile; 1,6-dihydropyrimidine-5-carbonitrile; 2,3-dihydropyridazine-4-carbonitrile; 3-amino-thiophene-2-carboxylate; 3-amino-thiophene-2-carbonitrile; 3,4-diaminothieno[2,3-b] thiophene-2,5-dicarbo- nitrile; 2-(3-bromo-1-iodoisoquinolin-8-yl) benzonitrile and 3-mercapto-benzo[g]quinolin-4(1H)-one derivatives. The synthesis of the tetrahydrothieno [3, 2-b] quinoline derivatives were explained through the following chemical reactions: Aldol condensation, alkylation, cyclocondensation, dehydration, chlorination, Wolff-Kishner reduction, acylation, Friedlander reaction and intramolecular cyclization.

Molecular dynamics study of enhanced autophosphorylation by S904F mutation of the RET kinase domain

The aberrant kinase activity of RET (rearranged during transfection), a transmembrane tyrosine kinase, is associated with human cancer. A point mutation caused by the replacement of solvent-front hydrophilic S904, located on the activation loop (A-loop), with a bulky hydrophobic phenylalanine residue can induce resistance to the type I kinase inhibitor vandetanib. A possible mechanism of this drug resistance is the release of a cis-autoinhibited conformation of RET for autophosphorylation, which activates RET kinase. Because the association between S904F mutation and enhanced autophosphorylation is unclear, we conducted molecular modeling analysis to compare unphosphorylated apo wild-type and S904F mutant structures. The structural compactness of the A-loop promoted ATP binding. When the A-loop is extended, the αC helix moves toward the glycine-rich loop, resulting in the protrusion of F735. The extruded F735 connects with E734 and R912 and constrains the ATP pocket entrance. Contrarily, a contracted A-loop pulls the αC helix away from the glycine-rich loop, burying F734 and making the ATP pocket accessible. The mutated F904 stabilizes the contracted A-loop and releases the autoinhibited conformation of RET, thereby facilitating autophosphorylation. We also simulated two ATP-bound systems. The binding free energies of ATP, estimated through the molecular mechanics with a generalized Born and surface area solvation approach, revealed that the S904F mutant was bound more tightly than was the wild type with the ATP. The findings support the premise of autophosphorylation promotion in the S904F mutant.

Recent developments of RET protein kinase inhibitors with diverse scaffolds as hinge binders

RET is a proto-oncogene encoding a receptor tyrosine kinase. RET regulates key aspects of cellular proliferation, differentiation and survival. The activation of RET via gene fusions or point mutations is closely related to lung, thyroid and other cancers. This review summarizes the developments of a diversity of small molecule RET protein kinase inhibitors in the past 10 years. These RET inhibitors are classified according to their hinge binder chemotypes as: pyrimidines, including the pyrazolopyrimidines, pyrimidine oxazines, quinazolines, 4-aminopyrimidines and 4-aminopyridines; indolinones; 5-aminopyrazole-4-carboxamides; 3-trifluoromethylanilines; imidazopyridines, imidazopyridazines and pyrazopyridines; nicotinonitriles; pyridones and 1,2,4-triazoles. In each section, the biological activities of the inhibitors, their structure-activity relationships and possible binding modes with the RET kinase are introduced.

Modifications on the Amino-3,5-dicyanopyridine Core To Obtain Multifaceted Adenosine Receptor Ligands with Antineuropathic Activity

A new series of amino-3,5-dicyanopyridines (1-31) was synthesized and biologically evaluated in order to further investigate the potential of this scaffold to obtain adenosine receptor (AR) ligands. In general, the modifications performed have led to compounds having high to good human (h) A₁AR affinity and an inverse agonist profile. While most of the compounds are hA₁AR-selective, some derivatives behave as mixed hA₁AR inverse agonists/A_2A and A_2B AR antagonists. The latter compounds (9-12) showed that they reduce oxaliplatin-induced neuropathic pain by a mechanism involving the alpha7 subtype of nAchRs, similar to the nonselective AR antagonist caffeine, taken as the reference compound. Along with the pharmacological evaluation, chemical stability of methyl 3-(((6-amino-3,5-dicyano-4-(furan-2-yl)pyridin-2-yl)sulfanyl)methyl)benzoate 10 was assessed in plasma matrices (rat and human), and molecular modeling studies were carried out to better rationalize the available structure-activity relationships.

The molecular basis for RET tyrosine-kinase inhibitors in thyroid cancer

RET receptor tyrosine kinase acts as a mutated oncogenic driver in several human malignancies and it is over-expressed in other cancers. Small molecule compounds with RET tyrosine kinase inhibitory activity are being investigated for the targeted treatment of these malignancies. Multi-targeted compounds with RET inhibitory concentration in the nanomolar range have entered clinical practice. This review summarizes mechanisms of RET oncogenic activity and properties of new compounds that, at the preclinical stage, have demonstrated promising anti-RET activity.

Recent Developments on Ultrasound-Assisted Synthesis of Bioactive N-Heterocycles at Ambient Temperature

N-Heterocycles represent privileged structural subunits well distributed in naturally occurring compounds with immense biological activities. The last decade has seen a tremendous practice to carry out reactions at ambient temperature avoiding harsh reaction conditions. By applying ultrasonic radiation in organic synthesis we can make synthetic protocols more sustainable and can carry out reactions at room temperature avoiding the traditional thermal harsh reaction conditions. Therefore the synthesis of biologically relevant N-heterocycles at room temperature under the influence of ultrasonic irradiation is one of the advancing areas in the 21st century among organic chemists. The present review summarises the latest developments on ultrasound-assisted synthesis of biologically relevant N-heterocycles at ambient temperature.

2-Methylpyridinium 2-carboxy-6-nitrobenzoate

In the title molecular salt, C6H8N+·C8H4NO6−, the pyridine ring is protonated at the N atom and the anion is deprotonated at one of the hydroxy O atoms. The dihedral angle between the planes of the benzene and pyridine rings is 8.45 (9)°. In the anion, the deprotonated carboxylate group is twisted at an angle of 73.78 (11)° from the attached benzene ring, whereas the carboxy group is slightly oriented at an angle of 14.98 (10)°. N—H...O and O—H...O hydrogen bonds link the anions and cations into an infinite chain along thecaxis and these chains are further consolidated by C—H...O hydrogen bonds to form a three-dimensional network. The crystals structure is also influenced by weak π–π interactions [centroid–centroid distance = 3.9055 (9) Å].

Crystal structure of 2-benzyl-amino-4-(4-bromo-phen-yl)-6,7-di-hydro-5H-cyclo-penta-[b]pyridine-3-carbo-nitrile

In the title compound C22H18BrN3, the cyclo-pentane ring adopts an envelope conformation with the central methyl-ene C atom as the flap. The dihedral angles between the central pyridine ring and the pendant benzyl and and bromo-benzene rings are 82.65 (1) and 47.23 (1)°, respectively. In the crystal, inversion dimers linked by pairs of N-H⋯Nn (n = nitrile) hydrogen bonds generate R 2 (2)(12) loops. These dimers are linked by weak π-π inter-actions [centroid-centroid distance = 3.7713 (14) Å] into a layered structure.

Selective inhibition of RET mediated cell proliferation in vitro by the kinase inhibitor SPP86

BACKGROUND

The RET tyrosine kinase receptor has emerged as a target in thyroid and endocrine resistant breast cancer. We previously reported the synthesis of kinase inhibitors with potent activity against RET. Herein, we have further investigated the effect of the lead compound SPP86 on RET mediated signaling and proliferation. Based on these observations, we hypothesized that SPP86 may be useful for studying the cellular activity of RET.

METHODS

We compared the effects of SPP86 on RET-induced signaling and proliferation in thyroid cancer cell lines expressing RET-PTC1 (TPC1), or the activating mutations BRAFV600E (8505C) and RASG13R (C643). The effect of SPP86 on RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK pathway signaling and cell proliferation in MCF7 breast cancer cells was also investigated.

RESULTS

SPP86 inhibited MAPK signaling and proliferation in RET/PTC1 expressing TPC1 but not 8505C or C643 cells. In TPC1 cells, the inhibition of RET phosphorylation required co-exposure to SPP86 and the focal adhesion kinase (FAK) inhibitor PF573228. In MCF7 cells, SPP86 inhibited RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK signaling and estrogen receptorα (ERα) phosphorylation, and inhibited proliferation to a similar degree as tamoxifen. Interestingly, SPP86 and PF573228 inhibited RET/PTC1 and GDNF- RET induced activation of Akt and MAPK signaling to a similar degree.

CONCLUSION

SPP86 selectively inhibits RET downstream signaling in RET/PTC1 but not BRAFV600E or RASG13R expressing cells, indicating that downstream kinases were not affected. SPP86 also inhibited RET signaling in MCF7 breast cancer cells. Additionally, RET- FAK crosstalk may play a key role in facilitating PTC1/RET and GDNF- RET induced activation of Akt and MAPK signaling in TPC1 and MCF7 cells.

Identification of two novel RET kinase inhibitors through MCR-based drug discovery: design, synthesis and evaluation

From an MCR fragment library, two novel chemical series have been developed as inhibitors of RET, which is a kinase involved in the pathology of medullary thyroid cancer (MTC). Structure activity relationship studies (SAR) identified two sub-micromolar tractable leads, 6g and 13g. 6g was confirmed to be a Type-II RET inhibitor. 13g and 6g inhibited RET in cells transformed by RET/C634. A RET DFG-out homology model was established and utilized to predict Type-II inhibitor binding modes.

Crystal structure of 2-(2-bromo-phen-yl)-4-(1H-indol-3-yl)-6-(thio-phen-2-yl)pyridine-3-carbo-nitrile

In the title compound, C24H14BrN3S, the dihedral angles between the planes of the pyridine ring and the pendant thio-phene ring, the indole ring system (r.m.s. deviation = 0.022 Å) and the bromo-benzene ring are 9.37 (17), 21.90 (12) and 69.01 (15)°, respectively. The approximate coplanarity of the central ring and the indole ring system is supported by two intra-molecular C-H⋯N inter-actions. In the crystal, inversion dimers linked by pairs of N-H⋯N hydrogen bonds generate R 2 (2)(16) loops and the dimers are linked by C-H⋯π and aromatic π-π stacking [shortest centroid-centroid separation = 3.729 (3) Å] into a three-dimensional network.

Synthesis and properties of a selective inhibitor of homeodomain-interacting protein kinase 2 (HIPK2)

Homeodomain-interacting protein kinase 2 (HIPK2) is a Ser/Thr kinase controlling cell proliferation and survival, whose investigation has been hampered by the lack of specific inhibitors able to dissect its cellular functions. SB203580, a p38 MAP kinase inhibitor, has been used as a tool to inhibit HIPK2 in cells, but here we show that its efficacy as HIPK2 inhibitor is negligible (IC₅₀>40 µM). In contrast by altering the scaffold of the promiscuous CK2 inhibitor TBI a new class of HIPK2 inhibitors has been generated. One of these, TBID, displays toward HIPK2 unprecedented efficacy (IC₅₀ = 0.33 µM) and selectivity (Gini coefficient 0.592 out of a panel of 76 kinases). The two other members of the HIPK family, HIPK1 and HIPK3, are also inhibited by TBID albeit less efficiently than HIPK2. The mode of action of TBID is competitive with respect to ATP, consistent with modelling. We also provide evidence that TBID is cell permeable by showing that HIPK2 activity is reduced in cells treated with TBID, although with an IC₅₀ two orders of magnitude higher (about 50 µM) than in vitro.

Synthesis of alkynyl/alkenyl-substituted pyridine derivatives via heterocyclization and Pd-mediated Sonogashira/Heck coupling process in one-pot: a new MCR strategy

The present MCR strategy opens new avenues in the development of i) a diversity-oriented new cyanopyridine based compound library and ii) new chemical entities other than the present reported molecules.

6-(4-Aminophenyl)-2-methoxy-4-phenylnicotinonitrile

In the structure of the title nicotino­nitrile derivative, C₁₉H₁₅N₃O, the pyridine ring makes dihedral angles of 11.50 (7) and 43.36 (8)° with the 4-amino­phenyl and phenyl rings, respectively, and the dihedral angle between the phenyl rings is 36.28°. In the crystal, mol­ecules are linked by N—H⋯N hydrogen bonds into wave-like sheets parallel to (10-2). These sheets are stacked by π–π inter­actions between the 4-amino­phenyl rings of adjacent sheets, with centroid–centroid distances of 3.7499 (9) Å. C—H⋯π inter­actions are also present.

6-Methoxy-4-(2,4,5-trimethoxyphenyl)-2,2′-bipyridine-5-carbonitrile

In the title 3-cyano­pyridine derivative, C₂₁H₁₉N₃O₄, the 3-cyano-substituted pyridine ring forms dihedral angles of 2.35 (5) and 41.60 (5)° with the unsubstituted pyridine and 2,4,5-trimeth­oxy-substituted benzene rings, respectively. The dihedral angle between the unsubstituted pyridine and benzene rings is 39.84 (5)°. The meth­oxy groups form C_meth­yl—O—C—(C,N) torsion angles in the range 0.80 (15)–11.45 (15)°. In the crystal, mol­ecules related by 2₁ screw axes are linked by weak C—H⋯N hydrogen bonds along [010]. In addition, weak C—H⋯π inter­actions and π–π stacking inter­actions between pyridine rings, with a centroid–centroid distance of 3.6448 (6) Å, are observed.

Synthesis and anticancer activity of di(3-thienyl)methanol and di(3-thienyl)methane

Di(3-thienyl)methanol (2) and di(3-thienyl)methane (3) have been synthesized and screened against the T98G (brain cancer) cell line. Treatment induced cell death (MTT and macro-colony assay), growth inhibition, cytogenetic damage (micronuclei formation), were studied as cellular response parameters. Treatment with the compounds enhanced growth inhibition and cell death in a concentration dependent manner in both T98G and HEK (normal) cell lines. At higher concentrations (>20 µg/mL) the cytotoxic effects of the compounds were highly significant. The effect on clonogenic capacity and micronuclei formation observed after treatment of cells. Amongst the compounds, compound 2 exhibited potent activity against T98G brain cancer cells. Despite potent in vitro activity, both compounds exhibited less cytotoxicity against normal human HEK cells at all effective concentrations.

6-(4-Aminophenyl)-4-(4-ethoxyphenyl)-2-methoxynicotinonitrile

In the title mol­ecule, C₂₁H₁₉N₃O₂, the central pyridine ring makes dihedral angles of 14.46 (9) and 34.67 (8)° with the 4-amino- and 4-eth­oxy-substituted benzene rings, respectively. The eth­oxy group is essentially coplanar with the attached benzene ring [C—O—C—C torsion angle = 178.70 (16)°] as is the meth­oxy group with the pyridine ring [C—O—C—N torsion angle = −3.0 (3)°]. In the crystal, mol­ecules are linked by N—H⋯N hydrogen bonds into chains along [201]. Weak C—H⋯O hydrogen bonds and C—H⋯π inter­actions are also present.

An efficient, microwave-assisted, one-pot synthesis of novel 5,6,7,8-tetrahydroquinoline-3-carbonitriles

An efficient, microwave-assisted synthesis of novel 2-alkoxy- 5,6,7,8-tetrahydroquinoline-3-carbonitriles, which have not hitherto been reported, via reactions of cyclohexanone and arylidene malononitriles in the corresponding alcohols in presence of sodium is described. All the newly synthesized compounds were characterized by the IR, 1H-NMR, 13C-NMR and mass spectroscopic techniques and by elemental analyses. The newly synthesized compounds were evaluated for their antibacterial and antifungal activities.