title: A macrocyclic peptide that serves as a cocrystallization ligand and inhibits the function of a MATE family transporter.
abstract: The random non-standard peptide integrated discovery (RaPID) system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound extrusion (PfMATE) transporter and inhibit the transport function. Moreover, these macrocyclic peptides were successfully employed as cocrystallization ligands of selenomethionine-labeled PfMATE. In this report, we disclose the details of the RaPID selection strategy that led to the identification of these three macrocyclic peptides as well as a fourth macrocyclic peptide, MaD8, which is exclusively discussed in this article. MaD8 was found to bind within the cleft of PfMATE's extracellular side and blocked the path of organic small molecules being extruded. The results of an ethidium bromide efflux assay confirmed the efflux inhibitory activity of MaD8, whose behavior was similar to that of previously reported MaD5.
authors.affiliation: Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Hipolito
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Takayuki
authors.initials: T
authors.lastname: Katoh
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Suga
mesh_terms: D000595:Amino Acid Sequence; D017920:Antiporters / Q000037:antagonists & inhibitors / Q000737:chemistry*; D019843:Archaeal Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray; D055808:Drug Discovery; D018432:Drug Resistance, Multiple; D004926:Escherichia coli; D004996:Ethidium / Q000378:metabolism; D005456:Fluorescent Dyes / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000737:chemistry / Q000494:pharmacology*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D020027:Pyrococcus furiosus / Q000378:metabolism*
chemical_list: D017920:Antiporters; D019843:Archaeal Proteins; D005456:Fluorescent Dyes; D008024:Ligands; D010456:Peptides, Cyclic; D004996:Ethidium