CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides

• Published in: Journal of chemical information and modeling Vol. 63; no. 7; pp. 2240 - 2250
• Main Authors: Li, Jianan, Yanagisawa, Keisuke, Sugita, Masatake, Fujie, Takuya, Ohue, Masahito, Akiyama, Yutaka
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 10.04.2023
• Subjects: Bioavailability; Bioinformatics; Cell Membrane Permeability; Data analysis; Data storage; Drug Design; Drug Discovery - methods; Macromolecules; Membranes; Peptides; Peptides - chemistry; Peptides, Cyclic - chemistry; Permeability; Proteins; Scientific visualization
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.2c01573

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.