Pharmacophore-based virtual screening, molecular dynamics simulations, and bioactivity validation for JAK1/TYK2 dual inhibitors

The JAK/STAT signaling pathway is a critical therapeutic target for autoimmune diseases. To overcome the safety limitations of pan-JAK inhibitors, dual JAK1/TYK2 inhibition has emerged as a promising strategy, aiming to maintain efficacy while minimizing JAK2-related hematological adverse effects. This study employed a computer-aided drug design approach, utilizing a dual-pharmacophore model for JAK1 and TYK2 to virtually screen a compound library. Subsequent functional screening in IFN-α-stimulated Jurkat cells identified four hits that downregulated STAT1 and STAT3 phosphorylation. Subsequent kinase inhibition assays confirmed that two of these compounds, T6309 and T4428, act as potent dual inhibitors of JAK1 and TYK2, with T6309 displaying markedly higher potency than T4428. Molecular docking and dynamics simulations revealed that T6309 and T4428 forms stable interactions with both targets, correlating with their higher activity. Moreover, T6309 and T4428 exhibited favorable oral pharmacokinetic properties in rats, with T6309 showing high oral bioavailability. Collectively, our work identifies T6309 and T4428 as two novel, potent, and orally bioavailable dual JAK1/TYK2 inhibitors, providing promising leads candidate for the treatment of autoimmune diseases and validating this targeted inhibition strategy. • Discovery of two novel dual JAK1/TYK2 inhibitors, T6309 and T4428, via a dual-pharmacophore-based virtual screening strategy. • Both compounds demonstrate potent dual inhibitory activity in enzymatic assays and effectively suppress JAK/STAT signaling in cells. • Comprehensive molecular dynamics simulations reveal distinct but stable binding modes for both compounds, rationalizing their inhibitory profiles. • Favorable and complementary ADMET properties: T6309 shows excellent oral bioavailability, whereas T4428 presents a promising pharmacokinetic profile for further optimization.