Small molecule modulation of immune-mediated disorders
Date
2024
DOI
Authors
Version
Embargo Date
2027-10-01,2027-10-01
OA Version
Citation
Abstract
The immune system is a complex network of cells, tissues, and molecules, that serves as the frontline defense against pathogens and foreign antigens. Cytokines are key regulators for its function, orchestrating the complex interplay between immune cells. Disruptions in cytokine signaling can precipitate immune dysregulation, tipping the delicate balance between protective immunity and pathological inflammation. Cytokine imbalances, characterized by overexpression or dysregulated signaling, result in chronic inflammation, autoimmune disorders, and cancer. Simultaneously, dysregulated immune activation pathways, including those involving antigen-presenting cells and T-cell responses, contribute to the breakdown of immune tolerance and the onset of autoimmunity.The current suite of therapeutics for targeting soluble proinflammatory cytokines and receptor units consists of monoclonal antibodies which are often limited by an intravenous route of administration, low tissue penetration, off-target effects, non-specific elimination, immunogenicity, and high cost of production. Small molecule therapeutics have advantages such as oral administration and increased tissue penetration but pose challenges in discovery and development. To address this, rational drug design approaches utilizing high throughput screening and structure-based fragment identification can be employed.
Here, we describe potent new inhibitors for the cytokine IL-4 from structure-activity studies and we profiled a panel of 33 disease-relevant human cytokines to identify small-molecule ligands and inhibitors to survey their tractability for small-molecule modulation. Using a small-molecule microarray-based approach the binding preferences of each cytokine were compared against a collection of 65,000 drug and lead-like compounds From this screen, 841 key chemical chemotypes were identified that define structural motifs that bias for binding to specific cytokines. These chemotypes were further validated in thermal shift assays, resulting in 281 cytokine binders. Six cytokines were prioritized and established that novel, first-in-class inhibitors can be identified from these binders with potencies ranging from single-digit to double-digit micromolar in reporter and functional cellular assays. For the first time, these studies show that cytokines are broadly amenable to small-molecule binding and inhibition with key insights into the chemical structures that can enable the inhibition of specific cytokines.
Additionally, a structure-based fragment design was implemented targeting HLA-DQ8 for innovative therapies in type 1 diabetes mellitus (T1DM) to counter immune activation. Genetic predispositions result in autoreactive T cells evading negative selection, leading to the production of autoantibodies against insulin B (9:23) peptide, marking the presymptomatic stage. This stage often remains undiagnosed for months to years, varying among patients. It is succeeded by the symptomatic stage, characterized by a two-thirds reduction in β cell mass due to pancreatic infiltration.
Previous attempts to prevent T1DM onset have been hindered by unspecificity and immunosuppression. Recently, the FDA approved Anti-CD3, a monoclonal antibody, to delay symptomatic stage T1DM onset in adults and pediatric patients aged 8 years and older. Diabetic HLA-DQ8 recognizes insulin B (9:23) peptide as a foreign antigen, triggering T cell receptor activation, clonal expansion, pancreatic infiltration, and eventual β cell death. The binding of diabetic HLA-DQ8 and insulin B (9:23) peptide involves three key interactions at the P1, P4, and P9 pockets. Leveraging structural insights into HLA-DQ8 and insulin B (9:23) peptide interactions, our structure-based fragment design approach identified 16 binder fragments, offering the potential for precise immunomodulation in T1DM treatment.
In summary, novel potent small molecule inhibitors targeting dysregulated cytokine signaling were discovered and evaluated which will further advance drug discovery and development efforts. Furthermore, structure-based fragment design targeting HLA-DQ8 mediated immunoactivation in T1DM lays a critical foundation for the future development of HLA-DQ8-specific fragments. This approach offers a potential avenue for restoring balance within the immune system and represents a significant step forward in the quest for effective therapeutics against immune-mediated disorders.
Description
2024