Identification of a Small Molecule Compound with Targeted Binding Affinity to Tumor Necrosis Factor-Alpha

Abstract

Tumor Necrosis Factor-alpha (TNF-α), a pro-inflammatory cytokine, is associated with the pathogenesis of diverse injuries. Medications targeting the dysregulated TNF-α in the body have been extensively used. However, most TNF-α inhibitors are monoclonal antibodies, presenting diverse side effects and limitations. This research employed computer-based analysis to design a TNF-α inhibitor as a small-molecule compound and demonstrated it through related experiments. When TNFR binds to TNF-α, trimerization occurs, leading to downstream activation, resulting in cellular inflammatory responses or cell death. Our study commenced with a focus on inhibiting the formation of these TNF-α trimers, aiming to improve the uncontrolled functionality of TNF-α. Our designed compound aimed to bind within the TNF-α trimer's pocket, a validation supported by docking tests conducted with the MOE interface and confirmed through SPR analysis. Additionally, we demonstrated that this compound inhibits TNF-α inflammatory signaling in cell-based experiments. Considering its notably low cytotoxicity, there is potential for it to act significantly as a TNF-α inhibitor within the body. Moreover, through structural analysis of the lead compound, we identified residues that seem to exhibit a meaningful impact as TNF-α inhibitors. These findings suggest new prospects for our research in both the small molecule compound market and pathological investigations. Keywords : Tumor Necrosis Factor-alpha, Small molecule compound inhibitor, Trimerization, docking, SEAP assay