Discovery and SAR of novel 4-thiazolyl-2-phenylaminopyrimidines as potent inhibitors of spleen tyrosine kinase (SYK)

Discovery and optimization of 4-pyrazolyl-2-aminopyrimidine derivatives as potent spleen tyrosine kinase (SYK) inhibitors

Spleen tyrosine kinase (Syk) is a key signal transduction mediator of the B cell receptor (BCR) signaling pathway. Abnormal BCR signaling plays a key role in initiation and development of B-cell-derived hematological malignancies, therefore, Syk represents a potential target for inhibiting the BCR signaling resulting in a therapeutic effect in these cancers. Herein, we describe a novel series of SYK inhibitors with 4-(3'-pyrazolyl)-2-amino-pyrimidine scaffold. Extensive study of structure-activity relationships led to the identification of 1 (NMS-0963), a highly potent Syk inhibitor (IC50 = 3 nM) endowed with high selectivity within a panel of tested kinases and high antiproliferative activity in SYK-dependent BaF3-TEL/SYK cells and in other BCR-dependent hematological tumor cell lines. Additionally, 1 effectively inhibited Syk phosphorylation and downstream signaling mediators of the BCR in treated cells. In in vivo pharmacokinetics studies, 1, displayed good pharmacokinetics properties, with linear exposure with dose and excellent oral bioavailability. These findings suggest that 1 is a promising new Syk inhibitor for treating BCR-dependent hematological cancers.

3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors

Spleen tyrosine kinase (SYK) is an essential mediator of immune cell signaling and has been anticipated as a therapeutic target for autoimmune diseases, notably rheumatoid arthritis, allergic rhinitis, asthma, and cancers. Significant attempts have been undertaken in recent years to develop SYK inhibitors; however, limited success has been achieved due to poor pharmacokinetics and adverse effects of inhibitors. The primary goal of this research was to identify potential inhibitors having high affinity, selectivity based on key molecular interactions, and good drug-like properties than the available inhibitor, fostamatinib. In this study, a 3D-QSAR model was built for SYK based on known inhibitor IC₅₀ values. The best pharmacophore model was then used as a 3D query to screen a drug-like database to retrieve hits with novel chemical scaffolds. The obtained compounds were subjected to binding affinity prediction using the molecular docking approach, and the results were subsequently validated using molecular dynamics (MD) simulations. The simulated compounds were ranked according to binding free energy (ΔG), and the binding affinity was compared with fostamatinib. The binding mode analysis of selected compounds revealed that the hit compounds form hydrogen bond interactions with hinge region residue Ala451, glycine-rich loop residue Lys375, Ser379, and DFG motif Asp512. Identified hits were also observed to form a desirable interaction with Pro455 and Asn457, the rare feature observed in SYK inhibitors. Therefore, we argue that identified hit compounds ZINC98363745, ZINC98365358, ZINC98364133, and ZINC08789982 may help in drug design against SYK.

Discovery of a Potent Candidate for RET-Specific Non-Small-Cell Lung Cancer-A Combined In Silico and In Vitro Strategy

Rearranged during transfection (RET) is a tyrosine kinase oncogenic receptor, activated in several cancers including non-small-cell lung cancer (NSCLC). Multiple kinase inhibitors vandetanib and cabozantinib are commonly used in the treatment of RET-positive NSCLC. However, specificity, toxicity, and reduced efficacy limit the usage of multiple kinase inhibitors in targeting RET protein. Thus, in the present investigation, we aimed to figure out novel and potent candidates for the inhibition of RET protein using combined in silico and in vitro strategies. In the present study, screening of 11,808 compounds from the DrugBank repository was accomplished by different hypotheses such as pharmacophore, e-pharmacophore, and receptor cavity-based models in the initial stage. The results from the different hypotheses were then integrated to eliminate the false positive prediction. The inhibitory activities of the screened compounds were tested by the glide docking algorithm. Moreover, RF score, Tanimoto coefficient, prime-MM/GBSA, and density functional theory calculations were utilized to re-score the binding free energy of the docked complexes with high precision. This procedure resulted in three lead molecules, namely DB07194, DB03496, and DB11982, against the RET protein. The screened lead molecules together with reference compounds were then subjected to a long molecular dynamics simulation with a 200 ns time duration to validate the inhibitory activity. Further analysis of compounds using MM-PBSA and mutation studies resulted in the identification of potent compound DB07194. In essence, a cell viability assay with RET-specific lung cancer cell line LC-2/ad was also carried out to confirm the in vitro biological activity of the resultant compound, DB07194. Indeed, the results from our study conclude that DB07194 can be effectively translated for this new therapeutic purpose, in contrast to the properties for which it was originally designed and synthesized.

Highly potent and selective pyrazolylpyrimidines as Syk kinase inhibitors

A series of pyrazolylpyrimidine scaffold based Syk inhibitors were synthesized and evaluated for their biological activities and selectivity. Lead optimization efforts provided compounds with potent Syk inhibition in both enzymatic and TNF-α release assay.

Inhibitors of switch kinase 'spleen tyrosine kinase' in inflammation and immune-mediated disorders: a review

Spleen tyrosine kinase (Syk), a member of Syk family of non-receptor protein tyrosine kinases plays a significant role in the immune cell signaling in B cells, mast cells, macrophages and neutrophils. Anomalous regulation of this kinase can lead to different allergic disorders and antibody-mediated autoimmune diseases such as rheumatoid arthritis, asthma, psoriasis and allergic rhinitis. Being involved in the growth and survive mechanism of B cells, its inhibition can be beneficial in B-cell lymphoma. Thus, Syk can be sited as a therapeutically relevant target for various allergic and autoimmune disorders. This review article describes the structure of Syk and its role in B-cell signaling. In addition to this, data regarding small molecule inhibitors of Syk has also been reviewed from different papers and patents published.

Designing of new multi-targeted inhibitors of spleen tyrosine kinase (Syk) and zeta-associated protein of 70kDa (ZAP-70) using hierarchical virtual screening protocol

In the present study, diverse inhibitor molecules of two protein tyrosine kinases i.e. Syk and ZAP-70 were considered for the pharmacophore and docking analyses to design new multi-targeted agents for these enzymes. These enzymes are non-receptor protein tyrosine kinases and both are expressed mainly in B and T-lymphocytes where they play a crucial role in immune signaling. The role of these two enzymes in inflammatory and autoimmune diseases makes them potential therapeutic targets for the designing of new multi-targeted agents to combat disease conditions associated with them. The pharmacophore models were developed for Syk and ZAP-70 inhibitors using PHASE module of Schrödinger software. The generated pharmacophore models for both enzymes were clustered and top five models for each target were selected on the basis of survival minus inactive score that were subsequently used for the 3D-QSAR analysis. The best model for Syk (ADHR.45-5) and ZAP-70 (AADRR.265-3) were selected corresponding to highest value of Q(2). Both models were employed for the screening of a PHASE database of approximately 1.5 million compounds, subsequently the retrieved hits were screened employing docking simulations with Syk and ZAP-70 proteins. Finally, the screened compounds having structural features of both pharmacophore models and displaying essential interactions with both proteins were investigated for ADME properties. Thus, the new leads obtained in this way would show inhibitory activity against Syk and ZAP-70, and may serve as novel therapeutic agents for the treatment of inflammatory disorders.

Applying ligands profiling using multiple extended electron distribution based field templates and feature trees similarity searching in the discovery of new generation of urea-based antineoplastic kinase inhibitors

This study provides a comprehensive computational procedure for the discovery of novel urea-based antineoplastic kinase inhibitors while focusing on diversification of both chemotype and selectivity pattern. It presents a systematic structural analysis of the different binding motifs of urea-based kinase inhibitors and the corresponding configurations of the kinase enzymes. The computational model depends on simultaneous application of two protocols. The first protocol applies multiple consecutive validated virtual screening filters including SMARTS, support vector-machine model (ROC = 0.98), Bayesian model (ROC = 0.86) and structure-based pharmacophore filters based on urea-based kinase inhibitors complexes retrieved from literature. This is followed by hits profiling against different extended electron distribution (XED) based field templates representing different kinase targets. The second protocol enables cancericidal activity verification by using the algorithm of feature trees (Ftrees) similarity searching against NCI database. Being a proof-of-concept study, this combined procedure was experimentally validated by its utilization in developing a novel series of urea-based derivatives of strong anticancer activity. This new series is based on 3-benzylbenzo[d]thiazol-2(3H)-one scaffold which has interesting chemical feasibility and wide diversification capability. Antineoplastic activity of this series was assayed in vitro against NCI 60 tumor-cell lines showing very strong inhibition of GI₅₀ as low as 0.9 uM. Additionally, its mechanism was unleashed using KINEX™ protein kinase microarray-based small molecule inhibitor profiling platform and cell cycle analysis showing a peculiar selectivity pattern against Zap70, c-src, Mink1, csk and MeKK2 kinases. Interestingly, it showed activity on syk kinase confirming the recent studies finding of the high activity of diphenyl urea containing compounds against this kinase. Allover, the new series, which is based on a new kinase scaffold with interesting chemical diversification capabilities, showed that it exhibits its “emergent” properties by perturbing multiple unexplored kinase pathways.

Exploring the role of water molecules for docking and receptor guided 3D-QSAR analysis of naphthyridine derivatives as spleen tyrosine kinase (Syk) inhibitors

In the present study, 3D-QSAR analysis was performed utilizing docking based alignment of [1,6]-naphthyridine derivatives as Syk enzyme inhibitors. The role of the water molecules was explored for the docking based alignment that revealed two conserved water molecules important for proper orientation and alignment of naphthyridine inhibitors in the active site of Syk enzyme. The QSAR model was selected having highest value of Q(2) (0.624) and Pearson-r (0.862). The selected model also displayed the highest values of R(2) (0.978) and F-value (184.5) and the lowest SD (0.862). The contour plots developed on the basis of the best model helped to reveal the essential structural features of naphthyridines derivatives responsible for inhibition of Syk enzyme. The generated model and information revealed from it was utilized to design and predict new congeneric molecules that can be used as potential therapeutic agents.

Small-molecule protein and lipid kinase inhibitors in inflammation and specific models for their evaluation

The inflammatory response requires complex and coordinated cooperation of different signaling pathways and cell types. Therefore, more than 40 different protein or lipid kinases can be regarded as potential small-molecule inhibitor targets to approach a therapy of acute inflammation, such as septic syndrome, and especially chronic inflammation, such as rheumatoid arthritis or inflammatory bowel disease. Besides the general considerations about selectivity and potency of small-molecule kinase inhibitors, in this chapter special emphasis is put on the inflammation-specific methods and assays available for testing potential small-molecule inhibitors for their anti-inflammatory activity. Examples for human cell-based assays for characterization of the effect of inhibitors on contribution of various cell types, such as monocytes, neutrophils, mast cells, T-cells, and synovial fibroblasts, to the inflammatory scenario are given. It is further demonstrated how these assays are complemented by rodent models for septic syndrome, rheumatoid arthritis, ulcerative colitis, Crohn's disease, and systemic lupus erythematosus. Finally, it is discussed how the results obtained by these methods can be further validated and which future strategies for the treatment of chronic inflammation will exist.

A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are "docked" by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Data Bank and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and the experimental data for cases in which binding affinities differ by at least 1 order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol because of the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligands bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligands in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities.

Synthesis of New Peptidyl- and Glycosylpyrimidine Derivatives

A new series of 2- N-(phthalyl- or tosylamino acid)pyrimidines have been synthesised from the coupling of pyrimidine derivatives with phthalyl- or tosylamino acids. Hydrazinolysis of 2- N-phthalyl derivatives afforded unprotected amino acid derivatives. New derivatives of peptidylpyrimidines have been synthesised from the reaction of pyrimidine derivatives with α-amino acids methyl ester hydrochloride viz different routes. Also, new glycosides have been prepared from the reaction of pyrimidine derivatives with α-D-glucopyranosyl bromide. Most of the synthesised compounds showed a significant antimicrobial activity.

Spleen tyrosine kinases: biology, therapeutic targets and drugs

Spleen tyrosine kinase (Syk) is an intriguing protein tyrosine kinase involved in signal transduction in a variety of cell types, and its aberrant regulation is associated with different allergic disorders and antibody-mediated autoimmune diseases such as rheumatoid arthritis, asthma and allergic rhinitis. Syk also plays an important part in the uncontrolled growth of tumor cells, particularly B cells. For these reasons, Syk is considered one of the most interesting biological targets of the last decade, as proved by the great number of papers and patents published, and the possibility of treating these pathologies by means of Syk kinase inhibitors has led to a great interest from the pharmaceutical and biotech industry.

Therapeutic prospect of Syk inhibitors

BACKGROUND

The non-receptor spleen tyrosine kinase (Syk; EC 2.7.10.2) is involved in signal transduction in a variety of cell types. In particular, it is a key mediator of immune receptors signaling in host inflammatory cells (B cells, mast cells, macrophages and neutrophils), important for both allergic and antibody-mediated autoimmune diseases. Deregulated Syk kinase activity also allows growth factor-independent proliferation and transforms bone marrow-derived pre-B cells that are able to induce leukemia. Consequently, the development of Syk kinase inhibitors could conceivably treat these disorders and so they have became a major focus in the pharmaceutical and biotech industry.

OBJECTIVE

In this review, we analyze the structure and role of Syk kinase, the use of small molecules, interacting with ATP-binding site, as inhibitors of kinase activity and finally the potential of using inhibitors of Syk kinase expression to attenuate pathological conditions.

CONCLUSION

Syk kinase inhibition is suggested as a powerful tool for the therapy of different pathologies.

Targeting innate immunity protein kinase signalling in inflammation

Inflammation is an evolutionarily conserved host reaction that is initiated in response to trauma, tissue damage and infection. It leads to changes in tissue homeostasis and blood flow, immune-cell activation and migration, and secretion of cytokines and mediators in a spatio-temporally coordinated manner. Progress in understanding of the mechanisms of the inflammatory response has identified various protein kinases that act as essential signalling components and therefore represent potential therapeutic targets. This article summarizes advances in the identification and validation of such targets, and discusses key issues for the development of small-molecule kinase inhibitors as a new generation of oral anti-inflammatory drugs, including feedback loops, inhibitor specificity and combination therapy.

Pharmacophore modeling study based on known spleen tyrosine kinase inhibitors together with virtual screening for identifying novel inhibitors

In this investigation, chemical features based 3D pharmacophore models were developed based on the known inhibitors of Spleen tyrosine kinase (Syk) with the aid of hiphop and hyporefine modules within catalyst. The best quantitative pharmacophore model, Hypo1, was used as a 3D structural query for retrieving potential inhibitors from chemical databases including Specs, NCI, MayBridge, and Chinese Nature Product Database (CNPD). The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking studies to refine the retrieved hits. Finally 30 compounds were selected from the top ranked hit compounds and conducted an in vitro kinase inhibitory assay. Six compounds showed a good inhibitory potency against Syk, which have been selected for further investigation.