Preparation of 3-substituted-1-isopropyl-1H-pyrazolo[3,4-d]pyrimidin-4-amines as RET kinase inhibitors

A series of 3-substituted-1-isopropyl-1H-pyrazolo[3,4-d]pyrimidin-4-amines have been designed, synthesized, and evaluated as RET protein kinase inhibitors. On the basis of docking results, a small library of pyrazolopyrimidine compounds with an extended hydrophobic side arm was synthesized. The most promising of the compounds (7a) displayed efficient inhibition in vitro and good selectivity when tested on a panel of kinases. Furthermore, 7a inhibited GDNF-induced RET phosphorylation of ERK1/2 in MCF-7 breast cancer cells at concentrations as low as 100 nM.     

C4-substituted 1-beta-D-ribofuranosylpyrazolo[3,4-d]pyrimidines as adenosine agonist analogues

The synthesis of four novel C4-substituted 1-beta-D-ribofuranosylpyrazolo[3,4-d]pyrimidines is reported, and the compounds were examined as adenosine receptor agonist analogues. Neither receptor affinity nor biological activity was as potent as the purine counterparts. Adenosine agonists appear to be sensitive to modification of the purine base, with a nitrogen atom in the 7 position necessary for efficacy.     

Tyrosine kinase inhibitors. 18. 6-Substituted 4-anilinoquinazolines and 4-anilinopyrido[3,4-d]pyrimidines as soluble, irreversible inhibitors of the epidermal growth factor receptor.

4-Anilinoquinazoline- and 4-anilinopyrido[3,4-d]pyrimidine-6-acrylamides are potent pan-erbB tyrosine kinase inactivators, and one example (CI-1033) is in clinical trial. A series of analogues with a variety of Michael acceptor units at the 6-position were prepared to define the structural requirements for irreversible inhibition. A particular goal was to determine whether additional functions to increase solubility could be appended to the Michael acceptor. Substituted acrylamides were prepared by direct acylation of the corresponding 6-amines with the requisite acid or acid chloride. Vinylsulfonamide derivatives were obtained by acylation of the amines with chloroethylsulfonyl chloride followed by base-promoted elimination. Vinylsulfone and vinylsulfine derivatives were prepared by oxidation and base elimination of a hydroxyethylthio intermediate. The compounds were evaluated for their inhibition of phosphorylation of the isolated EGFR enzyme and for inhibition of EGF-stimulated autophosphorylation of EGFR in A431 cells and of heregulin-stimulated autophosphorylation of erbB2 in MDA-MB 453 cells. Substitution at the nitrogen of the acrylamide was tolerated only with a methyl group; larger substituents were dystherapeutic, and no substitution at all was tolerated at the acrylamide alpha-carbon. In contrast, while electron-donating groups at the acrylamide beta-carbon were not useful, even quite large electron-withdrawing groups (which increase its electrophilicity) were tolerated. A series of derivatives with solubility-enhancing substituents linked to the acrylamide beta-carbon via amides were potent irreversible inhibitors of isolated EGFR (IC50s = 0.4-1.1 nM), with weakly basic morpholine and imidazole derivatives being the best. Vinylsulfonamides were also potent and irreversible inhibitors, but vinylsulfones and vinylsulfines were reversible and only poorly active. Two compounds were evaluated against A431, H125, and MCF-7 xenografts in nude mice but were inferior in these assays to the clinical trial compound CI-1033.     

Synthesis and biological evaluation of 1-aryl-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-4-one inhibitors of cyclin-dependent kinases

Using a high-throughput screening strategy, a series of 1-aryl-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-4-ones was identified that inhibit the cyclin-dependent kinase (CDK) 4/cyclin D1 complex-mediated phosphorylation of a protein substrate with IC(50)s in the low micromolar range. On the basis of preliminary structure-activity relationships (SAR), a model was proposed in which these inhibitors occupy the ATP-binding site of the enzyme, forming critical hydrogen bonds to the same residue (Val96) to which the amino group in ATP is presumed to bind. X-ray diffraction studies on a later derivative bound to CDK2 support this binding mode. Iterative cycles of synthesis and screening lead to a novel series of potent, CDK2-selective 6-(arylmethyl)pyrazolopyrimidinones. Placement of a hydrogen-bond donor in the meta-position on the 6-arylmethyl group resulted in approximately 100-fold increases in CDK4 affinity, giving ligands that were equipotent inhibitors of CDK4 and CDK2. These compounds exhibit antiproliferative effects in the NCI HCT116 and other cell lines. The potency of these antiproliferative effects is enhanced in anilide derivatives and translates into tumor growth inhibition in a mouse xenograft model.     

Synthesis and biological activity of some 4-substituted 1-[1-(2,3-dihydroxy-1-propoxy)methyl-1,2,3-triazol-(4 & 5)-ylmethyl]-1H-pyrazolo[3,4-d]pyrimidines

Cycloaddition of 7a, b with 6 gave, after separation and deprotection, two regioisomers 10a, b and 11a, b. The deprotected acyclic nucleoside 10a used as the precursor for the preparation of 4-amino (12), 4-methylamino (13), 4-benzylamino (14), 4-methoxy (15) and 4-hydroxy (16) analogues. All acyclic nucleosides were evaluated for their inhibitory effects against HIV-1(IIIB), HIV-2(ROD) in MT-4 cells, for their anti-tumor activity and for their inhibitory effects against Mycobacterium tuberculosis. No marked activity was found.     

5,6,7-trisubstituted 4-aminopyrido[2,3-d]pyrimidines as novel inhibitors of adenosine kinase

The synthesis and structure-activity relationship of a series of 5,6,7-trisubstituted 4-aminopyrido[2,3-d]pyrimidines as novel nonnucleoside adenosine kinase inhibitors is described. A variety of alkyl, aryl, and heteroaryl substituents were found to be tolerated at the C5, C6, and C7 positions of the pyridopyrimidine core. These studies have led to the identification of analogues that are potent inhibitors of adenosine kinase with in vivo analgesic activity.     

QSAR study of 1,3–dioxo-4-methyl-2,3-dihydro-1h-pyrrolo[3,4-c]quinolines as caspase-3 inhibitors

Neurodegenerative disorders are consequences of progressive and irreversible loss of neurons due to unwanted apoptosis, which involves caspases, a group of cystein proteases that cleave other proteins and inactivate them. Among several different groups of caspase enzymes, caspases-3 play a key role in apoptosis. Therefore they are used as therapeutic target for their inhibitors. In pursuit of better caspase-3 inhibitors, a quantitative structure–activity relationship analysis was performed on a series of 1,3-dioxo-4-methyl-2, 3-dihydro-1H-pyrrolo [3,4-c] quinolines as caspase-3 inhibitors using WIN CAChe 6.1 and Medicinal Chemistry Regression Machine. The best QSAR model was selected and validated. The values of the statistical data are r = 0.951, F = 65.62, SEE = 0.4175, t = 2.08. The study reveals that, if the partition coefficient (log P), conformational minimum energy (CME), and the lowest unoccupied molecular orbital energy (E _LUMO) are altered, the biological activity is increased. On the basis of the selected QSAR model, we designed a new series of compounds, calculated their activity, and found that the compounds were more potent than existing compounds.     

Dihydropyrrole[2,3-d]pyridine derivatives as novel corticotropin-releasing factor-1 antagonists: mapping of the receptor binding pocket by in silico docking studies

In an effort to discover novel CRF-1 receptor antagonists exhibiting improved physicochemical properties, a dihydropirrole[2,3]pyridine scaffold was designed and explored in terms of the SAR of the substitution at the pendent phenyl ring and the nature of the heterocyclic moieties present in the upper region of the molecule. Selective and potent compounds have been discovered endowed with reduced ClogP with respect to compounds known in the literature. Of particular relevance was the finding that the in vitro affinity of the series was maintained by reducing the overall lipophilicity. The results achieved by this exploration enabled the formulation of a novel hypothesis on the nature of the receptor binding pocket of this class of CRF-1 receptor antagonists, making use of in silico docking studies of the putative nonpeptidic antagonist binding site set up in house by homology modeling techniques.     

Structure-based optimization of pyrazolo[3,4-d]pyrimidines as Abl inhibitors and antiproliferative agents toward human leukemia cell lines

Results from molecular docking calculations and Grid mapping laid the foundations for a structure-based optimization approach to improve the biological properties of pyrazolo-pyrimidine derivatives in terms of inhibition of Abl enzymatic activity and antiproliferative properties toward human leukemia cells. Insertion of halogen substituents with various substitution patterns, suggested by simulations, led to a significant improvement of leukemia cell growth inhibition and to an increase up to 1 order of magnitude of the affinity toward Abl.     

Molecular modeling studies on 3,4-dihydroquinazolines as trypanothione reductase inhibitors using 3D-QSAR and docking approaches

The trypanothione reductase (TryR) has been used as a key validated target to guide drug discovery for human African trypanosomiasis (HAT). 3D-QSAR and docking studies were performed on a series of 3,4-dihydroquinazolines as TryR inhibitors to establish a molecular model for new drug design. The CoMFA and CoMSIA models resulted from 53 molecules gave r _cv ² values of 0.591 and 0.574, r ² values of 0.968 and 0.943, respectively. The external validation indicated that CoMSIA model with a valid r _m ² value of 0.864 exhibited better predictive power than CoMFA model. 3D contour maps generated from CoMFA and CoMSIA along with the docking analyses have identified several key features responsible for the activity. A set of analogs were proposed by utilizing the results revealed in the present study, and were predicted with significantly improved potencies in the developed models. The results can be served as a useful guideline for designing novel 3,4-dihydroquinazoline derivatives with improved activity against human African trypanosomes.     

3D QSAR CoMFA/CoMSIA and docking studies on azole dione derivatives, as anti-cancer inhibitors

Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were performed on a series of 103 azole dione derivatives, as selective anti-cancer inhibitors. The atom and shape based root mean square alignment yielded the best predictive CoMFA model q2 = 0.923, r2 = 0.980, when compared with the CoMSIA model. Docking studies were employed to position the inhibitors into active site of Crystal Structure of Delta (4)-3-ketosteroid 5-beta-reductase (PDB id: 3BUR). Results that indicate steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor substituents play a significant role in design novel, potent and selective anti-cancer activity of the compounds.     

Tyrosine kinase inhibitors. 19. 6-Alkynamides of 4-anilinoquinazolines and 4-anilinopyrido[3,4-d]pyrimidines as irreversible inhibitors of the erbB family of tyrosine kinase receptors

Structure-activity relationships for inhibition of erbB1, erbB2, and erbB4 were determined for a series of alkynamide analogues of quinazoline- and pyrido[3,4-d]pyrimidine-based compounds. The compounds were prepared by coupling the appropriate 6-aminoquinazolines or 6-aminopyrido[3,4-d]pyrimidines with alkynoic acids, using EDCI.HCl in pyridine. The compounds showed pan-erbB enzyme inhibition but were on average about 10-fold more potent against erbB1 than against erbB2 and erbB4. For cellular inhibition, the nature of the alkylating side chains was an important determinant, with 5-dialkylamino-2-pentynamide type Michael acceptors providing the highest potency. This is suggested to be due to an improved ability of the amine to participate in an autocatalysis of the Michael reaction with enzyme cysteine residues. Pyrido[3,4-d]pyrimidine analogue 39 was selected for in vivo evaluation and achieved tumor regressions at 10 mg/kg in the A431 human epidermoid carcinoma and at 40 mg/kg for the SF767 human glioblastoma and the SKOV3 human ovarian carcinoma. Complete stasis was observed at 40 mg/kg in the BXPC3 human pancreatic carcinoma as well as in the H125 human non-small-cell lung carcinoma.