Structure-Guided Discovery and Preclinical Assessment of Novel (Thiophen-3-yl)aminopyrimidine Derivatives as Potent ERK1/2 Inhibitors.

The RAS-RAF-MEK-ERK signaling cascade is abnormally activated in various tumors, playing a crucial role in mediating tumor progression. As the key component at the terminal stage of this cascade, ERK1/2 emerges as a potential antitumor target and offers a promising therapeutic strategy for tumors harboring BRAF or RAS mutations. Here, we identified 36c with a (thiophen-3-yl)aminopyrimidine scaffold as a potent ERK1/2 inhibitor through structure-guided optimization for hit 18. In preclinical studies, 36c showed powerful ERK1/2 inhibitory activities (ERK1/2 IC50 = 0.11/0.08 nM) and potent antitumor efficacy both in vitro and in vivo against triple-negative breast cancer and colorectal cancer models harboring BRAF and RAS mutations. 36c could directly inhibit ERK1/2, significantly block the phosphorylation expression of their downstream substrates p90RSK and c-Myc, and induce cell apoptosis and incomplete autophagy-related cell death. Taken together, this work provides a promising ERK1/2 lead compound for multiple tumor-treatment drug discovery.

Synthesis and biological assessment of new pyrimidopyrimidines as inhibitors of breast cancer resistance protein (ABCG2).

Multidrug resistance constitutes a serious obstacle of the treatment success of cancer by chemotherapy. Mostly it is driven by expression of ABC transport proteins that actively efflux the anticancer agents out of the cell. This work describes the design and synthesis of 12 new pyrimidopyrimidines, as well as their inhibition of ABCG2 a transporter referred also to as breast cancer resistance protein, the selectivity versus ABCB1 (P-glycoprotein/P-gp) and ABCC1 as well as the investigation of their accumulation in single cells. From these results, N-(3,5-dimethoxyphenyl)-2-methyl-7-phenyl-5-(p-tolyl)pyrimido[4,5-d]pyrimidin-4-amine 7 h was identified as promising hit that deserves further investigation showing a selective and effective inhibition of ABCG2 with IC50 equal to 0.493 µM only 2-fold less active than Ko143.

Preparation, biological & cheminformatics-based assessment of N2,N4-diphenylpyrimidine-2,4-diamine as potential Kinase-targeted antimalarials.

Twenty eight new N2,N4-diphenylpyrimidine-2,4-diamines have been prepared in order to expand our understanding of the anti-malarial SAR of the scaffold. The aim of the study was to make structural modifications to improve the overall potency, selectivity and solubility of the series by varying the anilino groups attached to the 2- and 4-position. We evaluated the activity of the compounds against Plasmodium falciparum (Pf) 3D7, cytotoxicity against HepG2, % inhibition at a panel of 10 human kinases, solubility, permeability and lipophilicity, and human and rat in vitro clearance. 11 was identified as a potent anti-malarial with an IC50 of 0.66 µM at the 3D7 strain and a selectivity (SI) of ~ 40 in terms of cytotoxicity against the HepG2 cell line. It also displayed low experimental logD7.4 (2.27), reasonable solubility (124 µg/ml), good metabolic stability, but low permeability. A proteo-chemometric workflow was employed to identify putative Pf targets of the most promising compounds. Ligand-based similarity searching of the ChEMBL database led to the identification of most probable human targets. These were then used as input for sequence-based searching of the Pf proteome. Homology modelling and molecular docking were used to evaluate whether compounds could indeed bind to these targets with valid binding modes. In vitro biological testing against close human analogs of these targets was subsequently undertaken. This allowed us to identify potential Pf targets and human anti-targets that could be exploited in future development.

Biocatalysis in drug discovery and development.

Enzyme catalysis, enabled by advances in protein engineering and directed evolution, is beginning to transform chemical synthesis in the pharmaceutical industry. This review presents recent examples of the creative use of biocatalysis to enable drug discovery and development. We illustrate how increased access to novel biotransformations and the rise of cascade biocatalysis allowed fundamentally new syntheses of novel medicines, representing progress toward more sustainable pharmaceutical manufacturing. Finally, we describe the opportunities and challenges the industry must address to ensure the reduction to practice of biotechnological innovations to develop new therapies in a faster, more economical, and environmentally benign way.

Utility of Lauroyl Isothiocyanate as a Scaffold in the Synthesis of Some Novel Pyrimidine Derivatives and Their Antimicrobial Assessment.

The reaction of lauroyl isothiocyanate 1 with enaminonitrile derivative 2 furnished N-(6-cyano-3, 4-diphenylthieno[2,3-c]pyridazin-5-yl-carbamothioyl)dodecanamide 3, which was used as precursor for the synthesis of novel heterocyclic systems. Polyfunctional pyrimidine and fused pyrimidine derivatives were obtained by the cyclization of compound 3 under different basic conditions as well as its reactions with thiourea, o-aminothiophenol, hydrazine hydrate, phenyl hydrazine, ethyl phenyl acetate or ethyl benzoyl acetate. The structures of the new compounds were confirmed by microanalytical and spectral properties. The synthesised compounds were tested in-vitro for their antimicrobial activity and showed congruent results against most of the tested microorganisms compared to the standard drugs Gentamycin and Ketoconazol.

An efficient synthesis of pyrimidine specific 2'-deoxynucleoside-5'-tetraphosphates.

An efficient chemical synthesis of pyrimidine specific 2'-deoxynucleoside-5'-tetraphosphates, such as 2'-deoxycytidine-5'-tetraphosphate (dC4P) and thymidine-5'-tetraphosphate (T4P) is described. The present three-step synthetic strategy involves monophosphorylation of 2'-deoxynucleoside using phosphorous oxychloride, conversion of 5'-monophosphate into the corresponding imidazolide salt, followed by reaction with tris[tributylammonium] triphosphate leading to the 2'-deoxynucleoside-5'-tetraphosphate in good yields.

Assessment of antiplatelet activity of 2-aminopyrimidines.

A series of 4,6-diaryl-2-aminopyrimidines was developed as antiplatelet agents and their potency was evaluated by in vitro assay. Compound 14k was found to be two times more potent than aspirin. These encouraging results could be helpful for the development of new antiplatelet compounds.

Efficient one-pot, three-component synthesis of a library of pyrrolo[1,2-c]pyrimidine derivatives.

Herein is reported a simple and efficient one-pot three-component synthesis of pyrrolo[1,2-c]pyrimidine derivatives starting from various substituted pyrimidines, 2-bromoacetophenones, and electron deficient alkynes in epoxides acting both as reaction medium and HBr scavanger. This method proved to be very lucrative and avoids formation of ylide inactivation products. The synthesis represents an environmentally benign alternative to classical methods. The new library of compounds was briefly characterized regarding the improved Lipinski rule to asses the potential drug-likeness of the compounds. The majority of compounds are statisfing the Lipinski rule.

Chromeno[2,3-d]pyrimidine-triones synthesis by a three-component coupling reaction.

A simple and one-pot synthesis of new chromeno[2,3-d]pyrimidine-triones by a three-component condensation reaction of barbituric acids, aldehydes and cyclohexane-1,3-diones in refluxing ethanol in the presence of p-toluenesulfonic acid (p-TSA) for 3-10 h is reported. Two cyclohexane-1,3-diones, four barbituric acids and six substituted aldehydes were chosen for the library validation. Prominent among the advantages of this new method are operational simplicity, good yields and easy work-up procedures employed.

Medicinal chemistry strategies in follow-on drug discovery.

Drug discovery targeting novel mechanisms has become extremely expensive and risky. The annual first-in-class drug approvals have not been satisfactory in the past decade (two to six per year) despite an increased R&D budget. Follow-on programs targeting proven mechanisms are less risky and costly but can produce drugs with meaningful differentiations and thus can play an important supporting role. This article will discuss the medicinal chemistry strategies that have been utilized by the pharmaceutical industry to exploit validated therapeutic targets.

New one-pot four-component synthesis of disubstituted pyrido[2,3-d]pyrimidine-6-carboxamide derivatives.

In this work, 1,2,3,4,5,8-hexahydro-1,3,7-trimethyl-2,4-dioxopyrido[2,3-d]pyrimidine-6-carboxamide derivatives were synthesized in a simple and efficient method from the four-component condensation reaction of diketene, an aliphatic or aromatic amine, an aromatic aldehyde, and 6-amino-1,3-dimethyluracil in the presence of a catalytic amount of p-toluenesulfonic acid under mild conditions at ambient temperature in high yields.

Examining the chirality, conformation and selective kinase inhibition of 3-((3R,4R)-4-methyl-3-(methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)-3-oxopropanenitrile (CP-690,550).

Here, we examine the significance that stereochemistry plays within the clinically relevant Janus kinase 3 (Jak3) inhibitor 1 (CP-690,550). A synthesis of all four enantiopure stereoisomers of the drug was carried out and an examination of each compound revealed that only the enantiopure 3R,4R isomer was capable of blocking Stat5 phosphorylation (Jak3 dependent). Each compound was profiled across a panel of over 350 kinases, which revealed a high level of selectivity for the Jak family kinases for these related compounds. Each stereoisomer retained a degree of binding to Jak3 and Jak2 and the 3R,4S and 3S,4R stereoisomers were further revealed to have binding affinity for selected members of the STE7 and STE20 subfamily of kinases. Finally, an appraisal of the minimum energy conformation of each stereoisomer and molecular docking at Jak3 was performed in an effort to better understand each compounds selectivity and potency profiles.

Synthesis and pharmacological assessment of derivatives of isoxazolo[4,5-d]pyrimidine.

A series of new 5-alkyl and 5-arylisoxazolo[4,5-d]pyrimidinones (5a-g, 6-8) were prepared from 4-amino-3-oxo-isoxazolidine-5-carboxylic acid amide. Some of the aryl derivatives of isoxazolo[4,5-d]pyrimidine were tested pharmacologically in comparison with Diazepam. Compounds 5b-d and 7 demonstrated interesting anxiolytic activity.

Synthesis and pharmacological characterization of novel analogues of the nicotinic acetylcholine receptor agonist (+/-)-UB-165.

(+/-)-UB-165 (1) is a potent neuronal nicotinic acetylcholine receptor (nAChR) ligand, which displays functional selectivity between nAChR subtypes. Using UB-165 as a lead structure, two classes of racemic ligands were synthesized and assessed in binding assays for three major nAChR subtypes (alpha4beta2, alpha3beta4, and alpha7). The first class of compounds comprises the three pyridine isomers 4-6, corresponding to the 3-, 2-, and 4-substituted pyridine isomers, respectively. Deschloro UB-165 (4) displayed a 2-3-fold decrease in affinity at alpha4beta2 and alpha3beta4 nAChR subtypes, as compared with (+/-)-UB-165, while at the alpha7 subtype a 31-fold increase in affinity was observed. At each of the nAChR subtypes, high affinity binding was dependent on the presence of a 3-substituted pyridine, and the other isomers, 5 and 6, resulted in marked decreases in binding affinities. The second class of compounds is based on replacing the pyridyl unit of 1 with a diazine moiety, giving pyridazine (7), pyrimidine (8), and pyrazine (9), which retain the "3-pyridyl" substructure. Modest reductions in binding affinity were observed for all of the diazine ligands at all nAChR subtypes, with the exception of 7, which retained potency comparable to that of 4 in binding to alpha7 nAChR. In functional assays at the alpha3beta4 nAChR, all analogues 4-9 were less potent, as compared with 1, and the rank order of functional potencies correlated with that of binding potencies. Computational studies indicate that the 3-substituted pyridine 4 and 2-substituted pyridine 5, as well as the diazine analogues 7-9, all conform to a distance-based pharmacophore model recently proposed for the alpha4beta2 receptor. However, the nicotinic potencies of these ligands vary considerably and because 5 lacks appreciable nicotinic activity, it is clear that further refinements of this model are necessary in order to describe adequately the structural and electronic demands associated with this nAChR subtype. This rational series of compounds based on UB-165 presents a systematic approach to defining subtype specific pharmacophores.

An algorithm-directed two-component library synthesized via solid-phase methodology yielding potent and orally bioavailable p38 MAP kinase inhibitors.

Previously we reported the identification of RPR200765A, a potent orally bioavailable pyridine-imidazole inhibitor of p38 mitogen-activated protein (MAP) kinase which suppressed paw swelling and joint pathology in streptococcal cell wall-induced arthritis. Herein, we report the use of solid-phase combinatorial organic synthesis for the parallel processing of a related pyrimidine-imidazole-based library with two points of structural variability. We report also that the application of a computer algorithm, the Monte Carlo Monomer Selection, maximized both the combinatorial synthetic efficiency and the bioavailability of the final compounds. In conjunction with the synthetic protocols, the polymer-supported quench technique was applied to the purification of the final compounds. Through rapid evaluation of the library using a p38 kinase assay and permeability assays, it was possible to identify a number of potent and orally bioavailable p38 MAP kinase inhibitors suitable for further biological investigation.