Investigation on the chemical space of the substituted triazole thio-benzoxazepinone RIPK1 inhibitors

Discovery of a novel quinoline RIP1 inhibitor and its treatment of acute liver injury in mice

Necroptosis is closely associated with the development of inflammatory diseases, including acute liver injury. However, the precise role of necroptosis-related signature proteins in acute liver injury remains incompletely understood. Previously, our group investigated Compound o1, a RIP1 inhibitor, but its antinecroptosis activity and RIP1 binding affinity were suboptimal. In this study, we sought to address these two critical scientific challenges. Through a scaffold-hopping strategy, we identified a series of novel quinoline-like RIP1 inhibitors, among which N-1 exhibited the most potent antinecroptosis activity and the strongest RIP1 binding affinity. N-1 effectively inhibited necrosome formation by blocking phosphorylation in the RIP1/RIP3/MLKL signaling pathway. In a TNF-induced hypothermia mouse model of systemic inflammatory response syndrome (SIRS), N-1 significantly improved the survival rate of mice in a dose-dependent manner. Our study further revealed that RIP1, RIP3, and MLKL are expressed in normal liver tissues, whereas their phosphorylated forms (pRIP1, pRIP3, and pMLKL) are absent. In contrast, liver tissues from mice with CCl4-induced acute liver injury exhibited high expression levels of pRIP1, pRIP3, and pMLKL, indicating that necroptosis is associated with liver injury. N-1 significantly inhibited the phosphorylation of RIP1, RIP3, and MLKL, while restoring key liver damage markers such as alanine aminotransferase (ALT) and aspartate aminotransferase (AST). These findings suggest that targeting necroptosis may represent a promising therapeutic strategy for the treatment of acute liver injury.

Discovery and Characterization of Novel Receptor-Interacting Protein Kinase 1 Inhibitors Using Deep Learning and Virtual Screening

Receptor-interacting protein kinase 1 (RIPK1) serves as a critical mediator of cell necroptosis and represents a promising therapeutic target for various human neurodegenerative diseases and inflammatory diseases. Nonetheless, the RIPK1 inhibitors currently reported are inadequate for clinical research due to suboptimal inhibitory activities or lack of selectivity. Consequently, there is a need for the discovery of novel RIPK1 kinase inhibitors. In this study, we integrated a deep learning model, specifically the fingerprint graph attention network (FP-GAT), with molecular docking-based virtual screening to identify potential RIPK1 inhibitors from a library comprising 13 million compounds. Out of 43 compounds procured, two compounds (designated as 24 and 41) demonstrated enzyme inhibition activity exceeding 50% at a concentration of 10 μM against RIPK1. The half-maximal inhibitory concentrations (IC50) for compounds 24 and 41 were determined to be 2.01 and 2.95 μM, respectively. Furthermore, these compounds exhibited protective effects in an HT-29 cell model of TSZ-induced necroptosis, with half-maximal effective concentrations (EC50) of 6.77 μM for compound 24 and 68.70 μM for compound 41. Finally, molecular dynamics simulations and binding free energy calculations were conducted to elucidate the molecular mechanism of compounds 24 and 41 binding to RIPK1. The results show that Met92, Met95, Ala155, and Asp156 are key residues for novel RIPK1 inhibitors. In summary, this work discovered two hit compounds targeting RIPK1, which can be further structurally modified to become promising lead compounds.

Discovery of novel biaryl benzoxazepinones as dual-mode receptor-interacting protein kinase-1 (RIPK1) inhibitors

Systemic inflammatory response syndrome (SIRS), an exaggerated defense response of the organism to a noxious stressor, involves a massive inflammatory cascade that ultimately leads to reversible or irreversible end-organ dysfunction and even death. Suppressing RIPK1, a key protein in necroptosis pathway, has been proven to be an effective therapeutic strategy for inflammation and SIRS. In this study, a series of novel biaryl benzoxazepinone RIPK1 inhibitors were designed and synthesized by introducing different aryl substituents at the C7 position of benzoxazepinone. As a result, p-cyanophenyl substituted analog 19 exhibited the most potent in vitro anti-necroptotic effect in HT-29 cells (EC50 = 1.7 nM) and superior protection against temperature loss and death in mice in the TZ-induced SIRS model compared to GSK'772. What's more, in vivo analysis of the levels of inflammatory factors in mice also revealed that compound 19 had better anti-inflammatory activity than GSK'772.

Discovery of 4-amino-1,6-dihydro-7H-pyrrolo[2,3-d]pyridazin-7-one derivatives as potential receptor-interacting serine/threonine-protein kinase 1 (RIPK1) inhibitors

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important regulatory factor in the necroptosis signaling pathway, and is considered an attractive therapeutic target for treating multiple inflammatory diseases. Herein, we describe the design, synthesis, and structure-activity relationships of 4-amino-1,6-dihydro-7H-pyrrolo [2,3-d]pyridazin-7-one derivatives as RIPK1 inhibitors. Among them, 13c showed favorable RIPK1 kinase inhibition activity with an IC50 value of 59.8 nM, and high RIPK1 binding affinity compared with other regulatory kinases of necroptosis (RIPK1 Kd = 3.5 nM, RIPK3 Kd = 1700 nM, and MLKL Kd > 30,000 nM). 13c efficiently blocked TNFα-induced necroptosis in both human and murine cells (EC50 = 1.06-4.58 nM), and inhibited TSZ-induced phosphorylation of the RIPK1/RIPK3/MLKL pathway. In liver microsomal assay studies, the clearance rate and half-life of 13c were 18.40 mL/min/g and 75.33 min, respectively. 13c displayed acceptable pharmacokinetic characteristics, with oral bioavailability of 59.55%. In TNFα-induced systemic inflammatory response syndrome, pretreatment with 13c could effectively protect mice from loss of body temperature and death. Overall, these compounds are promising candidates for future optimization studies.

RIPK1 inhibitors: A key to unlocking the potential of necroptosis in drug development

Within the field of medical science, there is a great deal of interest in investigating cell death pathways in the hopes of discovering new drugs. Over the past two decades, pharmacological research has focused on necroptosis, a cell death process that has just been discovered. Receptor-interacting protein kinase 1 (RIPK1), an essential regulator in the cell death receptor signalling pathway, has been shown to be involved in the regulation of important events, including necrosis, inflammation, and apoptosis. Therefore, researching necroptosis inhibitors offers novel ways to treat a variety of disorders that are not well-treated by the therapeutic medications now on the market. The research and medicinal potential of RIPK1 inhibitors, a promising class of drugs, are thoroughly examined in this study. The journey from the discovery of Necrostatin-1 (Nec-1) to the recent advancements in RIPK1 inhibitors is marked by significant progress, highlighting the integration of traditional medicinal chemistry approaches with modern technologies like high-throughput screening and DNA-encoded library technology. This review presents a thorough exploration of the development and therapeutic potential of RIPK1 inhibitors, a promising class of compounds. Simultaneously, this review highlights the complex roles of RIPK1 in various pathological conditions and discusses potential inhibitors discovered through diverse pathways, emphasizing their efficacy against multiple disease models, providing significant guidance for the expansion of knowledge about RIPK1 and its inhibitors to develop more selective, potent, and safe therapeutic agents.

Insight from Linker Investigations: Discovery of a Novel Phenylbenzothiazole Necroptosis Inhibitor Targeting Receptor-Interacting Protein Kinase 1 (RIPK1) from a Phenoxybenzothiazole Compound with Dual RIPK1/3 Targeting Activity

Necroptosis, a regulated cell death form, is a critical contributor in various inflammatory diseases. We previously identified a phenoxybenzothiazole SZM-610 as a RIPK1 and RIPK3 necroptosis inhibitor. We conducted extensive studies to investigate different chemical components' effects on antinecroptosis activity and RIPK1/3 activity. This study focused on replacing the linker in phenoxybenzothiazoles to assess its impact. Remarkably, compound 10, bearing a novel 3,2'-phenylbenzothiazole scaffold, exhibited fourfold more potent nanomolar activity than SZM-610. Unlike SZM-610, this compound inhibited RIPK1 (Kd = 17 nM) and eliminated RIPK3 inhibition at 5000 nM. Various linkages confirmed the 3,2'-phenylbenzothiazole superior potency. Moreover, this compound specifically inhibited necroptosis by inhibiting RIPK1, RIPK3, and MLKL phosphorylation. In a TNF-induced inflammatory model, it dose-dependently (1.25-5 mg/kg) protected mice from hypothermia and death, surpassing SZM-610's effectiveness. These findings highlight 3,2'-phenylbenzothiazole as a promising lead structure for developing drugs targeting necroptosis-related diseases.

Discovery of Sibiriline derivatives as novel receptor-interacting protein kinase 1 inhibitors

Receptor-interacting protein kinase 1 (RIPK1), a vital protein of the necroptosis pathway, plays a pivotal role in various inflammatory diseases. Sibiriline has been reported to be a potent ATP-competitive RIPK1 inhibitor, but its anti-necroptotic effects are limited. A series of structural analogues of Sibiriline were synthesized and evaluated for their anti-necroptotic activity. Comprehensive structure-activity relationship (SAR) was performed to left azaindole and right substituents of benzene of Sibiriline, respectively. The optimal compound KWCN-41, specifically inhibiting cell necroptosis but not apoptosis, protects cell survival by blocking the necroptotic pathway, which inhibits the phosphorylation of essential proteins of the necroptosis. It also prevented the development of inflammation and reduced the level of inflammatory factors in mice. KWCN-41 is expected to be a lead compound for further studies in inflammatory diseases.

Structure-Based Design of Novel Alkynyl Thio-Benzoxazepinone Receptor-Interacting Protein Kinase-1 Inhibitors: Extending the Chemical Space from the Allosteric to ATP Binding Pockets

Systemic inflammatory response syndrome (SIRS), characterized by severe systemic inflammation, represents a major cause of health loss, potentially leading to multiple organ failure, shock, and death. Exploring potent RIPK1 inhibitors is an effective therapeutic strategy for SIRS. Recently, we described thio-benzoxazepinones as novel RIPK1 inhibitors and confirmed their anti-inflammatory activity. Herein, we further synthesized novel thio-benzoxazepinones by introducing substitutions on the benzene ring by an alkynyl bridge in order to extend the chemical space from the RIPK1 allosteric to ATP binding pockets. The in vitro cell and kinase assays found that compounds 2 and 29 showed highly potent activity against necroptosis (EC₅₀ = 3.7 and 3.2 nM) and high RIPK1 inhibitory activity (K_d = 9.7 and 70 nM). Prominently, these two analogues possessed better in vivo anti-inflammatory effects than the clinical candidate GSK'772 and effectively blocked hypothermia and deaths in a TNFα-induced SIRS model.

Profiling of the chemical space on the phenyl group of substituted benzothiazole RIPK3 inhibitors

Necroptosis is confirmed as a precisely programmed cell death that is activated in caspase-deficient conditions. Receptor-interacting protein kinase 1 (RIPK1), RIPK3 and mixed-lineage kinase domain-like pseudokinase (MLKL) are the key regulators involved in the signaling pathway. However, accumulating evidence suggests that RIPK1 also works in apoptosis and inflammation pathways independent of necroptosis. Differently, RIPK3 signals necroptosis independent of RIPK1. Thus, identification of specific RIPK3 inhibitors is of great importance for the drug development associated with necroptosis. The benzothiazole carboxamide is a privileged scaffold as RIPK3 inhibitors developed by our group recently. In this study, we work on the phenyl group in-between of benzothiazole and carboxamide to profile the chemical space. Finally, a chlorinated derivative XY-1-127 was found to specifically inhibit necroptosis rather than apoptosis with an EC₅₀ value of 676.8 nM and target RIPK3 with a K_d of 420 nM rather than RIPK1 (K_d = 4300 nM). It was also confirmed to block the formation of necrosome by inhibiting RIPK3 phosphorylation at 1 μM in necroptosis cells. This work discovers the chemical space insights on the phenyl group of the substituted benzothiazole RIPK3 inhibitors and provides a new lead compound for further development.