Structure-activity relationship studies of 5-benzylaminoimidazo[1,2-c]pyrimidine-8-carboxamide derivatives as potent, highly selective ZAP-70 kinase inhibitors

Discovery and Structural Optimization of Covalent ZAP-70 Kinase Inhibitors against Psoriasis

Psoriasis is a chronic inflammatory skin disease closely related with T cells, and its management remains a challenge. Novel targets and associated drugs are urgently needed. Zeta-chain-associated protein kinase 70 kDa (ZAP-70) has been recognized as a potential target for treating autoimmune diseases due to its crucial role in T cell receptor signaling. In our previous work, we identified a potent and selective covalent ZAP-70 inhibitor with anti-inflammatory activity in vitro. Herein, we report the structural optimization of covalent ZAP-70 inhibitors. Our efforts led to the discovery of compound 25 (RDN2150), which exhibited potent inhibitory activity against ZAP-70 and favorable selectivity. It also demonstrated promising inhibitory effects on T cell activation and inflammatory cytokine production. Furthermore, a topical application of 25 resulted in significant efficacy in an imiquimod-induced psoriasis mouse model. Overall, these findings present the basis of a promising strategy for the treatment of psoriasis by targeting ZAP-70.

Design and Synthesis of Triazole-Containing HDAC Inhibitors That Induce Antitumor Effects and Immune Response

Histone deacetylase (HDAC) is an epigenetic antitumor drug target, but most existing HDAC inhibitors show limited antitumor activity and their use is often accompanied by serious adverse effects. To overcome these problems, we designed and synthesized a series of triazole-containing compounds as novel HDAC inhibitors. Among them, compound 19h exhibited potent and selective inhibition of HDAC1, with good antiproliferative activity in vitro and an excellent pharmacokinetic profile. Compound 19h significantly inhibited the growth of human tumor xenografts in nude mice and murine tumor growth in immune-competent mice bearing MC38 colon cancer. In the MC38 model, 19h increased the ratio of splenic CD4⁺ T effector cells and promoted complete tumor regression in 5/6 animals when combined with the mPD-1 antibody. These results suggested that selective class I HDAC inhibitors exert direct tumor growth inhibition and indirect immune cell-mediated antitumor effects and are synergistic with immune checkpoint inhibitors.

Expanding the Diversity at the C-4 Position of Pyrido[2,3-d]pyrimidin-7(8H)-ones to Achieve Biological Activity against ZAP-70

Pyrido[2,3-d]pyrimidin-7(8H)-ones have attracted widespread interest due to their similarity with nitrogenous bases found in DNA and RNA and their potential applicability as tyrosine kinase inhibitors. Such structures, presenting up to five diversity centers, have allowed the synthesis of a wide range of differently substituted compounds; however, the diversity at the C4 position has mostly been limited to a few substituents. In this paper, a general synthetic methodology for the synthesis of 4-substituted-2-(phenylamino)-5,6-dihydropyrido[2,3-d]pyrimidin-7(8H)-ones is described. By using cross-coupling reactions, such as Ullmann, Buchwald–Hartwig, Suzuki–Miyaura, or Sonogashira reactions, catalyzed by Cu or Pd, we were able to describe new potential biologically active compounds. The resulting pyrido[2,3-d]pyrimidin-7(8H)-ones include N-alkyl, N-aryl, O-aryl, S-aryl, aryl, and arylethynyl substituents at C4, which have never been explored in connection with the biological activity of such heterocycles as tyrosine kinase inhibitors, in particular as ZAP-70 inhibitors.

Discovery of a potent, selective, and covalent ZAP-70 kinase inhibitor

ZAP-70 (zeta-chain associated protein kinase 70 kDa) signaling pathway and its functions have been involved in the development and adaptive immune signaling of T cell. It thus represents a promising target for autoimmune diseases. Although reversible ZAP-70 kinase domain inhibitors have been developed, they are either weak or nonselective. We report herein the structure-guided development of the first potent and covalent inhibitor of ZAP-70 kinase domain. In particular, compound 18 (RDN009) showed good selectivity for ZAP-70 over structurally related Syk, and displayed potent inhibitory effects on T cell proliferation, activation, and inflammatory cytokine production. A mass spectrometry analysis further confirmed the covalent linkage between the inhibitor and ZAP-70 protein at C346. Overall, the covalent inhibitor RDN009 represents a potent and selective probe of ZAP-70 for further development for treatment of autoimmune diseases.

An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies

Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work attempts to explore the structural basis of selective HDAC8 inhibition by docking, pharmacophore and 3 D QSAR studies of 53 highly potent and highly selective triazol-based hydroxamic acid inhibitors. The binding modes of these novel inhibitors have been explored via Glide XP (Extra Precision) and induced-fit docking (IFD) strategies. The IFD poses of highly active and selective inhibitors showed conformational changes in active site residues like Trp141, Phe152 and Phe208, which were further verified by molecular dynamics simulations. A new CH-π interaction, which is atypical of HDAC inhibitors, was also observed in case of some highly selective inhibitors. Two pharmacophore models have been proposed; one highlights the structural basis of potency of these inhibitors and the other focuses on the selectivity. The corresponding QSAR models, obtained from alignment of the inhibitors as per the proposed pharmacophore models, are highly statistically significant. These models highlight the importance of size of the hydrophobic and aromatic groups present in the inhibitors and their contribution to activity of the inhibitors. The ADMET properties of the ligand library have also been analyzed and the predicted descriptors have been correlated with activity using principal components analysis to gain insight into the effect of pharmacokinetic properties on the activity.Communicated by Ramaswamy H. Sarma.

Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization

Lenvatinib is an oral multikinase inhibitor that selectively inhibits vascular endothelial growth factor (VEGF) receptors 1 to 3 and other proangiogenic and oncogenic pathway-related receptor tyrosine kinases. To elucidate the origin of the potency of lenvatinib in VEGF receptor 2 (VEGFR2) inhibition, we conducted a kinetic interaction analysis of lenvatinib with VEGFR2 and X-ray analysis of the crystal structure of VEGFR2-lenvatinib complexes. Kinetic analysis revealed that lenvatinib had a rapid association rate constant and a relatively slow dissociation rate constant in complex with VEGFR2. Co-crystal structure analysis demonstrated that lenvatinib binds at its ATP mimetic quinoline moiety to the ATP binding site and to the neighboring region via a cyclopropane ring, adopting an Asp-Phe-Gly (DFG)-"in" conformation. These results suggest that lenvatinib is very distinct in its binding mode of interaction compared to the several approved VEGFR2 kinase inhibitors.

Achromobacter denitrificans SP1 produces pharmaceutically active 25C prodigiosin upon utilizing hazardous di(2-ethylhexyl)phthalate

This first report describes the purification and identification of an orange-red pigment produced by Achromobacter denitrificans strain SP1 (isolated from sewage sludge heavily contaminated with plastics) during its growth in a simple basal salt medium supplemented with the hazardous di(2-ethylhexyl)phthalate (DEHP) blended in PVC blood bag (in situ) or free DEHP (ex situ) as carbon source. The cell-bound pigment was elucidated, characterized at molecular level, and described as an unusual 25C prodigiosin analog for the first time. At laboratory conditions (in flasks), the dry cell mass was 75.2mg/g blood bag, which upon extraction yielded 7.1mg prodigiosin; at this stage the pH of the medium was dropped from 7.2 to 3.5. Considering its pharmaceutical importance, taking 10 known prodigiosins as controls, this 25C prodigiosin was subjected to molecular docking studies, showed comparable and promising binding efficiencies with the crucial molecular human targets like cycloxygenase-2, ZAP-70 kinase and Jak-3 kinase.

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.

Signal transduction via the T cell antigen receptor in naïve and effector/memory T cells

T cells play an indispensable role in immune defense against infectious agents, but can also be pathogenic. These T cells develop in the thymus, are exported into the periphery as naïve cells and participate in immune responses. Upon recognition of antigen, they are activated and differentiate into effector and memory T cells. While effector T cells carry out the function of the immune response, memory T cells can last up to the life time of the individual, and are activated by subsequent antigenic exposure. Throughout this life cycle, the T cell uses the same receptor for antigen, the T cell Receptor, a complex multi-subunit receptor. Recognition of antigen presented by peptide/MHC complexes on antigen presenting cells unleashes signaling pathways that control T cell activation at each stage. In this review, we discuss the signals regulated by the T cell receptor in naïve and effector/memory T cells.

ZAP-70: an essential kinase in T-cell signaling

ZAP-70 is a cytoplasmic protein tyrosine kinase that plays a critical role in the events involved in initiating T-cell responses by the antigen receptor. Here we review the structure of ZAP-70, its regulation, its role in development and in disease. We also describe a model experimental system in which ZAP-70 function can be interrupted by a small chemical inhibitor.

New insights into T cell biology and T cell-directed therapy for autoimmunity, inflammation, and immunosuppression

T cell-directed therapies have become mainstays in the management of various autoimmune diseases and organ transplantation. The understanding of T cell biology has expanded greatly since the development of most agents currently in use. Here we discuss important recent discoveries pertaining to T helper cell differentiation, lineage commitment, and function. Within this context, we examine existing T cell-directed therapies, including new agents being evaluated in clinical and preclinical studies. We also use recent findings to speculate on novel targets.