{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T13:23:20Z","timestamp":1787405000266,"version":"build-2736575974"},"reference-count":31,"publisher":"American Chemical Society (ACS)","issue":"8","license":[{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI162961"],"award-info":[{"award-number":["R01 AI162961"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008522","name":"University of Illinois at Chicago","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100008522","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100029479","name":"Medicinal Chemistry Division, American Chemical Society","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100029479","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Type II proline-rich antimicrobial peptides have emerged as promising therapeutic candidates due to their ability to inhibit a previously undrugged stage of bacterial protein synthesis: translation termination. The recent characterization of the potent Type II proline-rich antimicrobial peptide, Pdi1, suggests that it may represent a promising therapeutic candidate; however, no information is available concerning its ribosome-binding activity. The lack of biochemical and biophysical assays to interrogate the binding affinities and mechanism of action of this class of peptides presents a bottleneck in the drug-discovery pipeline. In this study, we report the first characterization of the ribosome-binding kinetics of a Type II proline-rich antimicrobial peptide, for which we applied a biolayer interferometry assay to study the Pdi1\u2013ribosome interaction. Our results reveal slow dissociation kinetics, which indicates prolonged residence time in the ribosomal nascent peptide exit tunnel. Additionally, alanine scanning of the Pdi1 C-terminus revealed that specific residues are critical for ribosome binding and contribute to the rate of Pdi1 dissociation. These findings were validated in cell-based assays where alanine substitutions at these positions reduced antibiotic activity. We also demonstrated that a Pdi1 derivative, which lacks the third-to-last pharmacophoric residue, fails to inhibit translation termination, despite retaining a submicromolar minimum inhibitory concentration. These results demonstrate that select residues in the Pdi1 pharmacophore play a critical role in ribosome binding and dissociation, in addition to inhibiting translation termination.<\/jats:p>","DOI":"10.1021\/acschembio.6c00052","type":"journal-article","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T15:56:56Z","timestamp":1784822216000},"page":"1897-1905","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Determinants\nof Ribosome Binding for the\nAntimicrobial Peptide Pdi1"],"prefix":"10.1021","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3912-2828","authenticated-orcid":true,"given":"Trevor T.","family":"Dean","sequence":"first","affiliation":[{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60612"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alyah","family":"Ziyad","sequence":"additional","affiliation":[{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60612"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorota","family":"Klepacki","sequence":"additional","affiliation":[{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60612"]},{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60607"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4488-347X","authenticated-orcid":true,"given":"Jose\u0301 A.","family":"Villegas","sequence":"additional","affiliation":[{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60612"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5410-306X","authenticated-orcid":true,"given":"Terry W.","family":"Moore","sequence":"additional","affiliation":[{"name":"University of Illinois Chicago , , , ,","place":["Chicago, Illinois, United States, 60612"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,23]]},"reference":[{"key":"2026082208550621800_cit1","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1177\/2042098614554919","article-title":"Antimicrobial resistance:\nrisk associated with antibiotic\noveruse and initiatives to reduce the problem","volume":"5","author":"Llor","year":"2014","journal-title":"Ther. Adv. Drug Saf."},{"key":"2026082208550621800_cit2","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1179\/2047773215Y.0000000030","article-title":"Antimicrobial resistance:\na global\nmultifaceted phenomenon","volume":"109","author":"Prestinaci","year":"2015","journal-title":"Pathog. Global Health"},{"key":"2026082208550621800_cit3","doi-asserted-by":"publisher","first-page":"e201","DOI":"10.1016\/S2214-109X(23)00539-9","article-title":"The burden of bacterial antimicrobial resistance in the WHO African\nregion in 2019: a cross-country systematic analysis","volume":"12","author":"Sartorius","year":"2024","journal-title":"Lancet Global Health"},{"key":"2026082208550621800_cit4","doi-asserted-by":"publisher","first-page":"1864","DOI":"10.1016\/j.jiph.2021.11.005","article-title":"Prevalence of multidrug-resistant\nbacteria associated with polymicrobial infections","volume":"14","author":"Kim","year":"2021","journal-title":"J. Infect. Public Health"},{"key":"2026082208550621800_cit5","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2024.127839","article-title":"Hypervirulent\nand carbapenem-resistant Klebsiella pneumoniae: A global public health\nthreat","volume":"288","author":"Lei","year":"2024","journal-title":"Microbiol Res."},{"key":"2026082208550621800_cit6","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1038\/nsmb.3439","article-title":"An antimicrobial\npeptide that inhibits translation by trapping release factors on the\nribosome","volume":"24","author":"Florin","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026082208550621800_cit7","doi-asserted-by":"publisher","first-page":"5194","DOI":"10.1038\/s44319-024-00277-5","article-title":"Activity, structure,\nand diversity of Type II proline-rich antimicrobial peptides from\ninsects","volume":"25","author":"Huang","year":"2024","journal-title":"EMBO Rep."},{"key":"2026082208550621800_cit8","doi-asserted-by":"publisher","first-page":"e216","DOI":"10.1016\/S1473-3099(20)30327-3","article-title":"The value of antimicrobial peptides in the age of resistance","volume":"20","author":"Magana","year":"2020","journal-title":"Lancet Infect. Dis"},{"key":"2026082208550621800_cit9","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1111\/j.1365-2958.2007.05903.x","article-title":"Role of the Escherichia coli SbmA in the antimicrobial activity\nof proline-rich peptides","volume":"66","author":"Mattiuzzo","year":"2007","journal-title":"Mol. Microbiol."},{"key":"2026082208550621800_cit10","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/nbt.3418","article-title":"The quantitative and condition-dependent Escherichia coli proteome","volume":"34","author":"Schmidt","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2026082208550621800_cit11","doi-asserted-by":"publisher","first-page":"11831","DOI":"10.1021\/acs.jmedchem.3c00406","article-title":"Structure-Activity Relationships of the Antimicrobial\nPeptide Natural Product Apidaecin","volume":"66","author":"Skowron","year":"2023","journal-title":"J. Med. Chem."},{"key":"2026082208550621800_cit12","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1021\/cb300063v","article-title":"Api88 is a novel antibacterial\ndesigner\npeptide to treat systemic infections with multidrug-resistant Gram-negative\npathogens","volume":"7","author":"Czihal","year":"2012","journal-title":"ACS Chem. Biol."},{"key":"2026082208550621800_cit13","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1128\/AAC.01923-12","article-title":"Novel apidaecin 1b\nanalogs with superior serum stabilities for treatment of infections\nby gram-negative pathogens","volume":"57","author":"Berthold","year":"2013","journal-title":"Antimicrob. Agents\nChemother."},{"key":"2026082208550621800_cit14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2026465118","article-title":"Charting\nthe sequence-activity landscape of peptide inhibitors of translation\ntermination","volume":"118","author":"Baliga","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026082208550621800_cit15","doi-asserted-by":"publisher","first-page":"14747","DOI":"10.3390\/molecules181214747","article-title":"OxymaPure\/DIC:\nan efficient reagent for the synthesis of a novel series of 4-[2-(2-acetylaminophenyl)-2-oxo-acetylamino]\nbenzoyl amino acid ester derivatives","volume":"18","author":"El-Faham","year":"2013","journal-title":"Molecules"},{"key":"2026082208550621800_cit16","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.tetlet.2008.10.141","article-title":"N-terminus FITC labeling of peptides\non solid support: the truth behind the spacer","volume":"50","author":"Jullian","year":"2009","journal-title":"Tetrahedron Lett."},{"issue":"1","key":"2026082208550621800_cit17","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.bbrc.2006.11.017","article-title":"Efficient\nProtein Selection\nBased on Ribosome Display System with Purified Components","volume":"352","author":"Ohashi","year":"2007","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026082208550621800_cit18","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11040430","article-title":"Antimicrobial Activity\nand 70S Ribosome Binding of Apidaecin-Derived Api805 with Increased\nBacterial Uptake Rate","volume":"11","author":"Ludwig","year":"2022","journal-title":"Antibiotics"},{"key":"2026082208550621800_cit19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48027-4","article-title":"Multimodal binding\nand inhibition of bacterial ribosomes by the antimicrobial peptides\nApi137 and Api88","volume":"15","author":"Lauer","year":"2024","journal-title":"Nat. Commun."},{"key":"2026082208550621800_cit20","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/90802","article-title":"Cell-free translation\nreconstituted\nwith purified components","volume":"19","author":"Shimizu","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"2026082208550621800_cit21","doi-asserted-by":"publisher","first-page":"12236","DOI":"10.1002\/anie.201407145","article-title":"Insect-derived proline-rich\nantimicrobial\npeptides kill bacteria by inhibiting bacterial protein translation\nat the 70S ribosome","volume":"53","author":"Krizsan","year":"2014","journal-title":"Angew. Chem., Int. Ed."},{"issue":"6","key":"2026082208550621800_cit22","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23063150","article-title":"Influence of Substitutions\nin the Binding Motif of\nProline-Rich Antimicrobial Peptide ARV-1502 on 70S Ribosome Binding\nand Antimicrobial Activity","volume":"23","author":"Brakel","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"2026082208550621800_cit23","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1021\/acsinfecdis.9b00484","article-title":"Correlating\nDrug-Target Residence Time and Post-antibiotic Effect: Insight into\nTarget Vulnerability","volume":"6","author":"Davoodi","year":"2020","journal-title":"ACS Infect. Dis."},{"key":"2026082208550621800_cit24","doi-asserted-by":"publisher","first-page":"13673","DOI":"10.1073\/pnas.1717168115","article-title":"Kinetics of drug-ribosome\ninteractions defines the cidality of macrolide antibiotics","volume":"114","author":"Svetlov","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026082208550621800_cit25","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2024.1398964","article-title":"Application\nof bio-layer interferometry\nfor the analysis of ribosome-protein interactions","volume":"11","author":"Pandiarajan","year":"2024","journal-title":"Front. Mol. Biosci."},{"key":"2026082208550621800_cit26","doi-asserted-by":"publisher","DOI":"10.1088\/1367-2630\/1\/1\/006","article-title":"Single\nmolecule force spectroscopy\nby AFM indicates helical structure of poly(ethylene-glycol) in water","volume":"1","author":"Oesterhelt","year":"1999","journal-title":"New J. Phys."},{"key":"2026082208550621800_cit27","doi-asserted-by":"publisher","first-page":"1082","DOI":"10.1038\/s41589-023-01300-x","article-title":"Inhibition\nof translation termination by the antimicrobial peptide Drosocin","volume":"19","author":"Mangano","year":"2023","journal-title":"Nat. Chem. Biol."},{"key":"2026082208550621800_cit28","doi-asserted-by":"publisher","first-page":"391","DOI":"10.2174\/09298665113206660104","article-title":"Cellular uptake of apidaecin 1b and\nrelated analogs\nin Gram-negative bacteria reveals novel antibacterial mechanism for\nproline-rich antimicrobial peptides","volume":"21","author":"Berthold","year":"2014","journal-title":"Protein\nPept. Lett."},{"key":"2026082208550621800_cit29","first-page":"165","article-title":"Label-Free\nKinetic Analysis of an Antibody-Antigen Interaction Using Biolayer\nInterferometry","volume-title":"Methods in Molecular Biology","author":"Kumaraswamy","year":"2015"},{"key":"2026082208550621800_cit30","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.ab.2017.08.002","article-title":"Designing Binding Kinetic Assay on\nthe Bio-Layer Interferometry\n(BLI) Biosensor to Characterize Antibody-Antigen Interactions","volume":"536","author":"Kamat","year":"2017","journal-title":"Anal. Biochem."},{"key":"2026082208550621800_cit31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-55836-8","article-title":"The proline-rich\nantimicrobial peptide Api137 disrupts large ribosomal subunit assembly\nand induces misfolding","volume":"16","author":"Lauer","year":"2025","journal-title":"Nat. Commun."}],"container-title":["ACS Chemical Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acschembio.6c00052","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acbcct\/article-pdf\/21\/8\/1897\/66237648\/acschembio.6c00052.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acbcct\/article-pdf\/21\/8\/1897\/66237648\/acschembio.6c00052.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T12:55:22Z","timestamp":1787403322000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acbcct\/article\/21\/8\/1897\/5231244\/Molecular-Determinants-of-Ribosome-Binding-for-the"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,23]]},"references-count":31,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,7,23]]},"published-print":{"date-parts":[[2026,8,21]]}},"URL":"https:\/\/doi.org\/10.1021\/acschembio.6c00052","relation":{},"ISSN":["1554-8929","1554-8937"],"issn-type":[{"value":"1554-8929","type":"print"},{"value":"1554-8937","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,23]]}}}