{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T03:16:11Z","timestamp":1789701371115,"version":"4.0.1"},"reference-count":33,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2013,8,30]],"date-time":"2013-08-30T00:00:00Z","timestamp":1377820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>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\u2019s 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.<\/jats:p>","DOI":"10.3390\/molecules180910514","type":"journal-article","created":{"date-parts":[[2013,8,30]],"date-time":"2013-08-30T13:20:35Z","timestamp":1377868835000},"page":"10514-10530","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["A Macrocyclic Peptide that Serves as a Cocrystallization Ligand and Inhibits the Function of a MATE Family Transporter"],"prefix":"10.3390","volume":"18","author":[{"given":"Christopher","family":"Hipolito","sequence":"first","affiliation":[{"name":"Department of Chemistry, Graduate School of Science, the University of Tokyo,  7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshiki","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science,  the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takayuki","family":"Katoh","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Graduate School of Science, the University of Tokyo,  7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osamu","family":"Nureki","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science,  the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Suga","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Graduate School of Science, the University of Tokyo,  7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2013,8,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.jmb.2010.01.061","article-title":"Generation and characterization of a chimeric rabbit\/human Fab for co-crystallization of HIV-1 Rev","volume":"397","author":"Stahl","year":"2010","journal-title":"J. Mol. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.jsb.2006.09.006","article-title":"Searching for silver bullets: An alternative strategy for crystallizing macromolecules","volume":"156","author":"McPherson","year":"2006","journal-title":"J. Struct. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2012.12.010","article-title":"Generating conformation-specific synthetic antibodies to trap proteins in selected functional states","volume":"60","author":"Paduch","year":"2013","journal-title":"Methods"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1073\/pnas.1219901110","article-title":"Structures of a Na+-coupled, substrate-bound MATE multidrug transporter","volume":"110","author":"Lu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1021\/cg700702c","article-title":"Addressing the protein crystallization bottleneck by cocrystallization","volume":"7","author":"Warke","year":"2007","journal-title":"Cryst. Growth Des."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/S0969-2126(00)00152-0","article-title":"Structure at 2.3 \u00c5 resolution of the cytochrome bc1 complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment","volume":"8","author":"Hunte","year":"2000","journal-title":"Structure"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/35102009","article-title":"Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 \u00c5 resolution","volume":"414","author":"Zhou","year":"2001","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.jsb.2007.01.013","article-title":"In vitro selection and characterization of DARPins and Fab fragments for the co-crystallization of membrane proteins: The Na+-citrate symporter CitS as an example","volume":"159","author":"Huber","year":"2007","journal-title":"J. Struct. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"20395","DOI":"10.1074\/jbc.M112.359794","article-title":"Asymmetry in the homodimeric ABC transporter MsbA recognized by a DARPin","volume":"287","author":"Mittal","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1126\/science.4001944","article-title":"Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface","volume":"228","author":"Smith","year":"1985","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4937","DOI":"10.1073\/pnas.94.10.4937","article-title":"In vitro selection and evolution of functional proteins by using ribosome display","volume":"94","author":"Hanes","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2549","DOI":"10.1002\/cbic.201200493","article-title":"Two synthetic antibodies that recognize and neutralize distinct proteolytic forms of the ebola virus envelope glycoprotein","volume":"13","author":"Koellhoffer","year":"2012","journal-title":"Chembiochem"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/S0014-5793(97)01026-0","article-title":"In vitro virus: Bonding of mRNA bearing puromycin at the 3'-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro","volume":"414","author":"Nemoto","year":"1997","journal-title":"FEBS Lett."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"12297","DOI":"10.1073\/pnas.94.23.12297","article-title":"RNA-peptide fusions for the in vitro selection of peptides and proteins","volume":"94","author":"Roberts","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1016\/j.chembiol.2011.09.013","article-title":"Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library","volume":"18","author":"Yamagishi","year":"2011","journal-title":"Chem. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/j.chembiol.2003.10.010","article-title":"Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code","volume":"10","author":"Murakami","year":"2003","journal-title":"Chem. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1021\/ar2000953","article-title":"Flexizymes: Their evolutionary history and the origin of catalytic function","volume":"44","author":"Morimoto","year":"2011","journal-title":"Acc. Chem. Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth877","article-title":"A highly flexible tRNA acylation method for non-natural peptide synthesis","volume":"3","author":"Murakami","year":"2006","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/j.cbpa.2007.08.011","article-title":"The flexizyme system: A highly flexible tRNA aminoacylation tool for the translation apparatus","volume":"11","author":"Ohuchi","year":"2007","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/nprot.2011.331","article-title":"Flexizymes for genetic code reprogramming","volume":"6","author":"Goto","year":"2011","journal-title":"Nat. Protoc."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.cbpa.2007.12.009","article-title":"Synthesis of biopolymers using genetic code reprogramming","volume":"12","author":"Ohta","year":"2008","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1139\/O08-009","article-title":"Ribosomal Synthesis of nonstandard peptides","volume":"86","author":"Kang","year":"2008","journal-title":"Biochem. Cell. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.cbpa.2012.02.014","article-title":"Ribosomal Production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems","volume":"16","author":"Hipolito","year":"2012","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3423","DOI":"10.1002\/anie.201108118","article-title":"Discovery of macrocyclic peptides armed with a Mechanism-based warhead: Isoform-selective inhibition of human deacetylase SIRT2","volume":"51","author":"Morimoto","year":"2012","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_25","first-page":"607","article-title":"In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors","volume":"7","author":"Hayashi","year":"2012","journal-title":"Chem. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nature09408","article-title":"Structure of a cation-bound multidrug and toxic compound extrusion transporter","volume":"467","author":"He","year":"2010","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"17923","DOI":"10.1073\/pnas.0506483102","article-title":"A human transporter protein that mediates the final excretion step for toxic organic cations","volume":"102","author":"Otsuka","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1681\/ASN.2006030205","article-title":"Identification and functional characterization of a new human kidney-specific H+\/organic cation antiporter, kidney-specific multidrug and toxin extrusion 2","volume":"17","author":"Masuda","year":"2006","journal-title":"J. Am. Soc. Nephrol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/nature12014","article-title":"Structural basis for the drug extrusion mechanism by a MATE multidrug transporter","volume":"496","author":"Tanaka","year":"2013","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1021\/cb700233t","article-title":"Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides","volume":"3","author":"Goto","year":"2008","journal-title":"ACS Chem. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"5783","DOI":"10.1039\/c2ob25306b","article-title":"Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation","volume":"10","author":"Iwasaki","year":"2012","journal-title":"Org. Biomol. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.sbi.2011.06.007","article-title":"Lipidic cubic phase technologies for membrane protein structural studies","volume":"21","author":"Cherezov","year":"2011","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1128\/AAC.47.1.27-33.2003","article-title":"Contributions of MExAB-OprM and an EmrE homolog to intrinsic resistance of Pseudomonas aeruginosa to aminoglycosides and dyes","volume":"47","author":"Li","year":"2003","journal-title":"Antimicrob. Agents Chemother."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/18\/9\/10514\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T21:48:58Z","timestamp":1760219338000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/18\/9\/10514"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8,30]]},"references-count":33,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2013,9]]}},"alternative-id":["molecules180910514"],"URL":"https:\/\/doi.org\/10.3390\/molecules180910514","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,8,30]]}}}