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CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides
[Image: see text] Recently, cyclic peptides have been considered breakthrough drugs because they can interact with “undruggable” targets such as intracellular protein–protein interactions. Membrane permeability is an essential indicator of oral bioavailability and intracellular targeting, and the de...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091415/ https://www.ncbi.nlm.nih.gov/pubmed/36930969 http://dx.doi.org/10.1021/acs.jcim.2c01573 |
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author | Li, Jianan Yanagisawa, Keisuke Sugita, Masatake Fujie, Takuya Ohue, Masahito Akiyama, Yutaka |
author_facet | Li, Jianan Yanagisawa, Keisuke Sugita, Masatake Fujie, Takuya Ohue, Masahito Akiyama, Yutaka |
author_sort | Li, Jianan |
collection | PubMed |
description | [Image: see text] Recently, cyclic peptides have been considered breakthrough drugs because they can interact with “undruggable” targets such as intracellular protein–protein interactions. 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. |
format | Online Article Text |
id | pubmed-10091415 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100914152023-04-13 CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides Li, Jianan Yanagisawa, Keisuke Sugita, Masatake Fujie, Takuya Ohue, Masahito Akiyama, Yutaka J Chem Inf Model [Image: see text] Recently, cyclic peptides have been considered breakthrough drugs because they can interact with “undruggable” targets such as intracellular protein–protein interactions. 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. American Chemical Society 2023-03-17 /pmc/articles/PMC10091415/ /pubmed/36930969 http://dx.doi.org/10.1021/acs.jcim.2c01573 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Li, Jianan Yanagisawa, Keisuke Sugita, Masatake Fujie, Takuya Ohue, Masahito Akiyama, Yutaka CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides |
title | CycPeptMPDB: A
Comprehensive Database of Membrane
Permeability of Cyclic Peptides |
title_full | CycPeptMPDB: A
Comprehensive Database of Membrane
Permeability of Cyclic Peptides |
title_fullStr | CycPeptMPDB: A
Comprehensive Database of Membrane
Permeability of Cyclic Peptides |
title_full_unstemmed | CycPeptMPDB: A
Comprehensive Database of Membrane
Permeability of Cyclic Peptides |
title_short | CycPeptMPDB: A
Comprehensive Database of Membrane
Permeability of Cyclic Peptides |
title_sort | cycpeptmpdb: a
comprehensive database of membrane
permeability of cyclic peptides |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091415/ https://www.ncbi.nlm.nih.gov/pubmed/36930969 http://dx.doi.org/10.1021/acs.jcim.2c01573 |
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