Design and Synthesis of Novel, Non-ATP-Competitive MKK3 Modulators as Suppressors of TNF-α Production for the Treatment of Ulcerative Colitis

Although TNF-α is a clinically validated target for Ulcerative colitis (UC), therapy is dominated by injectable biologics, with no oral small-molecule inhibitors approved. Traditional ATP-competitive p38 inhibitors designed to regulate TNF-α have failed in clinical trials due to poor kinome selectivity. As the primary upstream activator of p38, MKK3 is considered a promising alternative target, but the development of small molecules remains limited, with a notable absence of non-ATP-competitive modulators. Herein, we report a series of compounds targeting the non-ATP-competitive pocket of MKK3 to suppress TNF-α production. Among them, (R)-48 was identified as a lead candidate, demonstrating robust suppression of TNF-α (IC50: 0.038 μM), high oral bioavailability (62.6%), clear dose-dependent efficacy and strong PK/PD relationships in mouse UC models. Particularly, HDX-MS suggested (R)-48 probably binds to a distal allosteric site on MKK3, precluding TAK1-mediated activation. Altogether, (R)-48 emerges as a promising oral small-molecule therapeutic candidate for the treatment of UC.