3-Amino-pyrazolo[3,4-d]pyrimidines as p38α kinase inhibitors: design and development to a highly selective lead

Discovery of novel (E)-1-methyl-9-(3-methylbenzylidene)-6,7,8,9-tetrahydropyrazolo[3,4-d]pyrido[1,2-a]pyrimidin-4(1H)-one as DDR2 kinase inhibitor: Synthesis, molecular docking, and anticancer properties

We report the synthesis, molecular docking and anticancer properties of the novel compound (E)-1-methyl-9-(3-methylbenzylidene)-6,7,8,9-tetrahydropyrazolo[3,4-d]pyrido[1,2-a]pyrimidin-4(1H)-one (PP562). PP562 was screened against sixteen human cancer cell lines and exhibited excellent antiproliferative activity with IC₅₀ values ranging from 0.016 to 5.667 μM. Experiments were carried out using the target PP562 at a single dose of 1.0 μM against a kinase panel comprising 100 different enzymes. A plausible binding mechanism for PP562 inhibition of DDR2 was determined using molecular dynamic analysis. The effect of PP562 on cell proliferation was also examined in cancer cell models with both high and low expression of the DDR2 gene; PP562 inhibition of high-expressing cells was more prominent than that for low expressing cells. PP562 also exhibits excellent anticancer potency toward the HGC-27 gastric cancer cell line. In addition, PP562 inhibits colony formation, cell migration, and adhesion, induces cell cycle arrest at the G2/M phase, and affects ROS generation and cell apoptosis. After DDR2 gene knockdown, the antitumor effects of PP562 on tumor cells were significantly impaired. These results suggested that PP562 might exert its inhibitory effect on HCG-27 proliferation through the DDR2 target.

Pyrazolo[3,4-d]pyrimidine scaffold: A review on synthetic approaches and EGFR and VEGFR inhibitory activities

The pyrazolo[3,4-d]pyrimidine core has received a lot of interest from the medicinal chemistry community as a promising framework for drug design and discovery. It is an isostere of the adenine ring of adenosine triphosphate, which allows it to mimic kinase active site hinge region binding contacts. This scaffold has a wide pharmacological and biological value, one of which is as an anticancer agent. Many successful anticancer medicines have been designed and synthesized using pyrazolo[3,4-d]pyrimidine as a key pharmacophore. The main synthetic routes of pyrazolo[3,4-d]pyrimidines as well as their recent developments as promising anticancer agents acting as endothelial growth factor receptors and vascular endothelial growth factor receptor inhibitors, published in the time frame from 1999 to 2022, are summarized in this review to set the direction for the design and synthesis of novel pyrazolo[3,4-d]pyrimidine derivatives for clinical deployment in cancer treatment.

Current status and future prospects of p38α/MAPK14 kinase and its inhibitors

P38α (which is also named MAPK14) plays a pivotal role in initiating different disease states such as inflammatory disorders, neurodegenerative diseases, cardiovascular cases, and cancer. Inhibitors of p38α can be utilized for treatment of these diseases. In this article, we reviewed the structural and biological characteristics of p38α, its relationship to the fore-mentioned disease states, as well as the recently reported inhibitors and classified them according to their chemical structures. We focused on the articles published in the literature during the last decade (2011-2020).

Design, synthesis and evaluation of some pyrazolo[3,4-d]pyrimidines as anti-inflammatory agents

New pyrazolo[3,4-d]pyrimidines substituted with various functionalities or attached to a substituted pyrazole ring through different linkages were synthesized. The synthesized compounds were evaluated for their anti-inflammatory activity using in vitro COX-1/COX-2 inhibition assay and in vivo formalin induced paw edema and cotton pellet-induced granuloma assays. Results revealed that compounds 17b and 18 possessed COX-1/COX-2 selectivity indices higher than diclofenac sodium and celecoxib. However, compounds 16a,b exhibited selectivity indices higher than diclofenac sodium and nearly equivalent to celecoxib, whereas, 9b displayed selectivity index comparable to diclofenac sodium. In vivo anti-inflammatory data showed that compounds 9b, 16a, 18 displayed anti-inflammatory activity higher than both references in the formalin induced paw edema model. On the other hand, the pyrazolyl derivatives 9b, 16b and 17b displayed anti-inflammatory activity about 2-2.5-fold that of diclofenac sodium and nearly 8-10.5-fold that of celecoxib in the cotton pellet-induced granuloma assay. The ulcerogenic effect of the active compounds was also investigated and results revealed that compounds 16a, 17a,b and 18 showed good gastrointestinal safety profile. Based on this, compounds 16a and 18 were considered as safe and effective leads in managing acute inflammation, while, 17b was prominent in controlling chronic inflammation.

A Comprehensive Structural Overview of p38α Mitogen-Activated Protein Kinase in Complex with ATP-Site and Non-ATP-Site Binders

Herein we review all the currently available ATP-site and non-ATP-site ligands bound to p38α mitogen-activated protein kinase (MAPK) available in the RCSB Protein Data Bank (PDB). The co-crystallized inhibitors have been classified into different families according to their experimental binding mode and chemical structure, and the ligand-protein interactions are discussed using the most representative compounds. This systematic structural analysis could provide some take-home lessons for drug discovery programs aimed at the rational identification and optimization of new p38α MAPK inhibitors.

RETRACTED: Design, synthesis, structure-activity relationship and kinase inhibitory activity of substituted 3-methyl-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-ones

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the author who confirmed that the purity of some of the described compounds is below acceptable standards and thus the biochemical results reported in the paper have no validity.

A Comprehensive Structural Overview of p38α MAPK in Complex with Type I Inhibitors

p38α mitogen-activated protein kinase (MAPK) is a well-recognized therapeutic target for the treatment of autoimmune and inflammatory diseases. Over the past two decades, tremendous efforts have been focused on the discovery and development of small-molecule p38α MAPK inhibitors, although currently no drugs targeting this protein are clinically available. Therefore, the identification of novel chemotypes that are able to inhibit p38α MAPK function is still of great therapeutic significance. With the objective to support drug discovery programs aimed at identifying new immunomodulators acting on p38α MAPK, herein we present a complete overview of the available crystal structures of this protein in complex with ATP-site type I inhibitors. The 85 available complexes are classified by chemotype and experimental binding mode, and the ligand-protein interactions are discussed using the most representative inhibitors. The type and frequency of key inhibitor features are analyzed to give a final summary of the chemical requirements of promising p38α MAPK inhibitors. The proposed pharmacophore can be exploited to enhance the opportunities to identify novel type I inhibitors of p38α MAPK.

Progress of the synthesis of condensed pyrazole derivatives (from 2010 to mid-2013)

Condensed pyrazole derivatives are important heterocyclic compounds due to their excellent biological activities and have been widely applied in pharmaceutical and agromedical fields. In recent years, numerous condensed pyrazole derivatives have been synthesized and advanced to clinic studies with various biological activities. In this review, we summarized the reported synthesis methods of condensed pyrazole derivatives from 2010 until now. All compounds are divided into three parts according to the rings connected to pyrazole-ring, i.e. [5, 5], [5,F 6], and [5, 7]-condensed pyrazole derivatives. The biological activities and applications in pharmaceutical fields are briefly introduced to offer an orientation for the design and synthesis of condensed pyrazole derivatives with good biological activities.

Fragment-based approaches to the discovery of kinase inhibitors

Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.

IL-13-induced airway mucus production is attenuated by MAPK13 inhibition

Increased mucus production is a common cause of morbidity and mortality in inflammatory airway diseases, including asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. However, the precise molecular mechanisms for pathogenic mucus production are largely undetermined. Accordingly, there are no specific and effective anti-mucus therapeutics. Here, we define a signaling pathway from chloride channel calcium-activated 1 (CLCA1) to MAPK13 that is responsible for IL-13-driven mucus production in human airway epithelial cells. The same pathway was also highly activated in the lungs of humans with excess mucus production due to COPD. We further validated the pathway by using structure-based drug design to develop a series of novel MAPK13 inhibitors with nanomolar potency that effectively reduced mucus production in human airway epithelial cells. These results uncover and validate a new pathway for regulating mucus production as well as a corresponding therapeutic approach to mucus overproduction in inflammatory airway diseases.

Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2% of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10% respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.