Computational Evaluation of Necrostatin-1 Analogues as Potential RIPK1 Inhibitors

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) regulates necroptotic cell death and sterile inflammation, representing an established therapeutic target for degenerative and inflammatory disorders. Here, three putative hydantoin-based analogues bearing distinctive N-substitutions—an ethylcyclobutyl derivative (Compound 1), an ethoxyphenylethyl analogue (Compound 2), and a 5-chloroindole (3-fluoro-4-methylbenzyl) derivative (Compound 3)—were investigated against the prototypical inhibitor Necrostatin-1 using virtual screening, induced-fit docking, 500 ns molecular dynamics simulations and pharmacokinetic profiling. Induced Fit Docking within the RIPK1 kinase domain indicated that Compound 3 (−9.1 kcal/mol) and Compound 1 (−7.9 kcal/mol) achieved favorable predicted binding scores surpassing Necrostatin-1 (−7.3 kcal/mol), whereas Compound 2 displayed a considerably weaker binding score (−4.1 kcal/mol). All-atom molecular dynamics simulations revealed that Compound 1 maintained high dynamic stability with ligand RMSD constrained to 1.2–2.0 Å and sustained hydrogen bonding with Leu157. Conversely, Compound 2 dissociated from the primary binding pocket, while Compound 3 deviated from its initial docking pose (RMSD 7.0–9.2 Å) to engage a secondary interaction network with Asn170, Glu171 and Lys45. In silico ADME profiling predicted that all three candidates comply with Lipinski and Veber drug-likeness criteria with high predicted intestinal absorption. These computational findings provide putative structural insights into kinase-ligand interactions, prioritizing candidate molecules for chemical synthesis and in vitro biological evaluation.