Matrix metalloproteinase 9 (MMP9) is a member of a large family of proteases that are secreted as inactive zymogens. It is a key regulator of the extracellular matrix, involved in the degradation of various extracellular matrix proteins. MMP9 plays a pathological role in a variety of inflammatory and oncology disorders and has long been considered an attractive therapeutic target. GS-5745, a potent, highly selective humanized monoclonal antibody inhibitor of MMP9, has shown promise in treating ulcerative colitis and gastric cancer. Here we describe the crystal structure of GS-5745⅐MMP9 complex and biochemical studies to elucidate the mechanism of inhibition of MMP9 by GS-5745. GS-5745 binds MMP9 distal to the active site, near the junction between the prodomain and catalytic domain, and inhibits MMP9 by two mechanisms. Binding to pro-MMP9 prevents MMP9 activation, whereas binding to active MMP9 allosterically inhibits activity.Human matrix metalloproteinase 9 (MMP9), 3 also referred to as gelatinase B, is a member of the MMP family, which are secreted from cells as inactive zymogens. The MMP family consists of ϳ25 members that share a common domain structure. The proenzyme (pro-MMP9) contains an N-terminal propeptide domain, a zinc-containing catalytic domain with an insertion of three fibronectin type II repeats, and a C-terminal hemopexin-like domain, which is connected to the catalytic domain by an O-glycosylated linker (1). The propeptide domain contains a conserved cysteine residue that coordinates the active site zinc, preventing substrate binding and catalysis. Stepwise proteolytic cleavage of the propeptide is required to generate catalytically competent MMP9 (2, 3). A related protease, MMP3, has been shown to activate MMP9 in vitro by cleaving between residues, Glu-59/Met-60 and Arg-106/Phe-107, releasing the prodomain (4, 5). Once active, MMP9 is capable of cleaving numerous substrates (6).In vivo, MMP9 activity is critical in remodeling components of the extracellular matrix, including collagen IV and laminin in the basement membrane (7). In addition to its role in extracellular matrix remodeling, MMP9 regulates other cellular processes, and its expression and secretion are up-regulated in pathological states such as cancer and chronic inflammation (7-13). MMP9 has also been shown to activate latent cytokines and growth factors and alter both trafficking and cell surface protein expression of both myeloid and lymphoid cells (14 -17).Because of its association with disease and correlation with poor prognosis in ulcerative colitis and colorectal cancer patients, MMP9 has long been considered a potential target for therapeutic intervention. Efforts to discover and develop safe and effective drugs selectively targeting MMP9 have been difficult due to the high structural conservation of the protease active site among MMP family members. A clinical stage, broad-spectrum peptidomimetic MMP inhibitor, marimastat, failed to meet efficacy end points and led to musculoskeletal syndrome in some patients (12,18).A...