title: Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton.
abstract: CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, the crystal structure of Arp2/3 complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off-target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its clinical use. Herein we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free-energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a threefold increase in inhibitory activity in vitro relative to 1. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization.
authors.affiliation: Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, USA.
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Baggett
authors.forename: Zoe
authors.initials: Z
authors.lastname: Cournia
authors.forename: Min Suk
authors.initials: MS
authors.lastname: Han
authors.forename: George
authors.initials: G
authors.lastname: Patargias
authors.forename: Adam C
authors.initials: AC
authors.lastname: Glass
authors.forename: Shih-Yuan
authors.initials: SY
authors.lastname: Liu
authors.forename: Brad J
authors.initials: BJ
authors.lastname: Nolen
mesh_terms: D008841:Actin Cytoskeleton / Q000187:drug effects* / Q000378:metabolism; D051376:Actin-Related Protein 2-3 Complex / Q000037:antagonists & inhibitors* / Q000378:metabolism; D000818:Animals; D002417:Cattle; D017076:Computer-Aided Design; D004305:Dose-Response Relationship, Drug; D008958:Models, Molecular; D015394:Molecular Structure; D054852:Small Molecule Libraries / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D013237:Stereoisomerism; D013329:Structure-Activity Relationship
chemical_list: D051376:Actin-Related Protein 2-3 Complex; D054852:Small Molecule Libraries