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Membrane permeability is an essential indicator of oral bioavailability and intracellular targeting, and the development of membrane-permeable peptides is a bottleneck in cyclic peptide drug discovery. Although many experimental data on membrane permeability of cyclic peptides have been reported, a comprehensive database is not yet available. A comprehensive membrane permeability database is essential for developing computational methods for cyclic peptide drug design. In this study, we constructed CycPeptMPDB, the first web-accessible database of cyclic peptide membrane permeability. We collected information on a total of 7334 cyclic peptides, including the structure and experimentally measured membrane permeability, from 45 published papers and 2 patents from pharmaceutical companies. To unambiguously represent cyclic peptides larger than small molecules, we used the hierarchical editing language for macromolecules notation to generate a uniform sequence representation of peptides. In addition to data storage, CycPeptMPDB provides several supporting functions such as online data visualization, data analysis, and downloading. CycPeptMPDB is expected to be a valuable platform to support membrane permeability research on cyclic peptides. CycPeptMPDB can be freely accessed at http:\/\/cycpeptmpdb.com.<\/jats:p>","DOI":"10.1021\/acs.jcim.2c01573","type":"journal-article","created":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T18:13:00Z","timestamp":1679076780000},"page":"2240-2250","source":"Crossref","is-referenced-by-count":107,"title":["CycPeptMPDB: A\nComprehensive Database of Membrane\nPermeability of Cyclic Peptides"],"prefix":"10.1021","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9004-5485","authenticated-orcid":true,"given":"Jianan","family":"Li","sequence":"first","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0224-0035","authenticated-orcid":true,"given":"Keisuke","family":"Yanagisawa","sequence":"additional","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]},{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6298-4055","authenticated-orcid":true,"given":"Masatake","family":"Sugita","sequence":"additional","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]},{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2103-6195","authenticated-orcid":true,"given":"Takuya","family":"Fujie","sequence":"additional","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]},{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0120-1643","authenticated-orcid":true,"given":"Masahito","family":"Ohue","sequence":"additional","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]},{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2863-8703","authenticated-orcid":true,"given":"Yutaka","family":"Akiyama","sequence":"additional","affiliation":[{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]},{"name":"Tokyo Institute of Technology , , , ,","place":["Meguro-ku, Tokyo, Japan, 152-8550"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,3,17]]},"reference":[{"key":"2026081804444329900_cit1","doi-asserted-by":"publisher","first-page":"bbab159","DOI":"10.1093\/bib\/bbab159","article-title":"Utilizing graph machine learning within drug discovery\nand development","volume":"22","author":"Gaudelet","year":"2021","journal-title":"Brief. Bioinform."},{"key":"2026081804444329900_cit2","doi-asserted-by":"publisher","first-page":"7264","DOI":"10.1158\/1078-0432.CCR-07-2184","article-title":"The challenge of\ndrugging undruggable targets in cancer:\nLessons learned from targeting BCL-2 family members","volume":"13","author":"Verdine","year":"2007","journal-title":"Clin. Cancer Res."},{"key":"2026081804444329900_cit3","doi-asserted-by":"publisher","first-page":"4167","DOI":"10.1021\/jacs.8b13178","article-title":"Macrocyclic Peptides\nas Drug Candidates: Recent Progress\nand Remaining Challenges","volume":"141","author":"Vinogradov","year":"2019","journal-title":"J. Am. Chem. Soc."},{"key":"2026081804444329900_cit4","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1093\/bioinformatics\/btab726","article-title":"Plasma protein\nbinding prediction focusing on residue-level features and circularity\nof cyclic peptides by deep learning","volume":"38","author":"Li","year":"2022","journal-title":"Bioinformatics"},{"key":"2026081804444329900_cit5","doi-asserted-by":"publisher","first-page":"3604","DOI":"10.1021\/acs.accounts.1c00391","article-title":"The RaPID Platform\nfor the Discovery of Pseudo-Natural Macrocyclic\nPeptides","volume":"54","author":"Goto","year":"2021","journal-title":"Acc. Chem. 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Commun."},{"key":"2026081804444329900_cit9","doi-asserted-by":"publisher","first-page":"10241","DOI":"10.1021\/acs.chemrev.9b00008","article-title":"Understanding Cell\nPenetration of\nCyclic Peptides","volume":"119","author":"Dougherty","year":"2019","journal-title":"Chem. Rev."},{"key":"2026081804444329900_cit10","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1016\/j.drudis.2016.02.005","article-title":"Quantifying the chameleonic\nproperties of macrocycles and other high-molecular-weight\ndrugs","volume":"21","author":"Whitty","year":"2016","journal-title":"Drug Discovery Today"},{"key":"2026081804444329900_cit11","doi-asserted-by":"publisher","first-page":"5231","DOI":"10.1002\/chem.201905599","article-title":"Solution Conformations Explain the Chameleonic Behaviour\nof Macrocyclic Drugs","volume":"26","author":"Danelius","year":"2020","journal-title":"Chem.\ue5f8Eur. 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Chem."},{"key":"2026081804444329900_cit16","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1021\/acs.jcim.8b00485","article-title":"Rationalization\nof the membrane permeability\ndifferences in a series of analogue cyclic decapeptides","volume":"59","author":"Witek","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2026081804444329900_cit17","doi-asserted-by":"publisher","first-page":"2952","DOI":"10.1021\/acs.jcim.9b00217","article-title":"Conformation and Permeability: Cyclic Hexapeptide Diastereomers","volume":"59","author":"Ono","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2026081804444329900_cit18","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1021\/acs.jcim.0c00803","article-title":"Membrane Permeability\nin Cyclic Peptides\nis Modulated by Core Conformations","volume":"61","author":"Cipcigan","year":"2021","journal-title":"J. Chem.\nInf. 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Biopharm."},{"key":"2026081804444329900_cit24","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1016\/j.xphs.2020.10.052","article-title":"Predicting the Permeability\nof Macrocycles from Conformational Sampling \u2013 Limitations of\nMolecular Flexibility","volume":"110","author":"Poongavanam","year":"2021","journal-title":"J. Pharm. Sci."},{"key":"2026081804444329900_cit25","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1021\/ja508766b","article-title":"Cell-permeable\ncyclic peptides from\nsynthetic libraries inspired by natural products","volume":"137","author":"Hewitt","year":"2015","journal-title":"J. Am. Chem. Soc."},{"key":"2026081804444329900_cit26","doi-asserted-by":"publisher","first-page":"21755","DOI":"10.1002\/ange.202004550","article-title":"Drug-Like Properties in Macrocycles above MW 1000:\nBackbone Rigidity versus Side-Chain Lipophilicity","volume":"132","author":"Furukawa","year":"2020","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026081804444329900_cit27","doi-asserted-by":"publisher","first-page":"2796","DOI":"10.1021\/ci3001925","article-title":"HELM: A hierarchical\nnotation language for complex biomolecule structure representation","volume":"52","author":"Zhang","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"2026081804444329900_cit28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13321-021-00512-4","article-title":"STOUT: SMILES to IUPAC names using\nneural machine translation","volume":"13","author":"Rajan","year":"2021","journal-title":"J. Cheminf."},{"key":"2026081804444329900_cit29","doi-asserted-by":"crossref","unstructured":"Townsend, C. E.; Naylor, M. R.; Jason, E.; Pye, C.\nR.; Schwochert, J. A.; Edmondson, Q.; Lokey, R.\nS.\n          The passive permeability\nlandscape around geometrically\ndiverse hexa- and heptapeptide macrocycles. ChemRxiv Preprint, 2020. 10.26434\/chemrxiv.13335941.v1.","DOI":"10.26434\/chemrxiv.13335941.v1"}],"container-title":["Journal of Chemical Information\nand Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.2c01573","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/63\/7\/2240\/8910830\/ci2c01573.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/63\/7\/2240\/8910830\/ci2c01573.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:02:48Z","timestamp":1787043768000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/63\/7\/2240\/850420\/CycPeptMPDB-A-Comprehensive-Database-of-Membrane"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,17]]},"references-count":29,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2023,3,17]]},"published-print":{"date-parts":[[2023,4,10]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.2c01573","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,17]]}}}