Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning
Abstract Motivation In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of...
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| Vydané v: | Bioinformatics Ročník 38; číslo 4; s. 1110 - 1117 |
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| Hlavní autori: | , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
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England
Oxford University Press
27.01.2022
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| ISSN: | 1367-4803, 1367-4811, 1460-2059, 1367-4811 |
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| Abstract | Abstract
Motivation
In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of a compound in drug discovery and design. However, due to structural differences, previous computational prediction methods developed for small-molecule compounds cannot be successfully applied to cyclic peptides, and methods for predicting the PPB rate of cyclic peptides with high accuracy are not yet available.
Results
Cyclic peptides are larger than small molecules, and their local structures have a considerable impact on PPB; thus, molecular descriptors expressing residue-level local features of cyclic peptides, instead of those expressing the entire molecule, as well as the circularity of the cyclic peptides should be considered. Therefore, we developed a prediction method named CycPeptPPB using deep learning that considers both factors. First, the macrocycle ring of cyclic peptides was decomposed residue by residue. The residue-based descriptors were arranged according to the sequence information of the cyclic peptide. Furthermore, the circular data augmentation method was used, and the circular convolution method CyclicConv was devised to express the cyclic structure. CycPeptPPB exhibited excellent performance, with mean absolute error (MAE) of 4.79% and correlation coefficient (R) of 0.92 for the public drug dataset, compared to the prediction performance of the existing PPB rate prediction software (MAE=15.08%, R=0.63).
Availability and implementation
The data underlying this article are available in the online supplementary material. The source code of CycPeptPPB is available at https://github.com/akiyamalab/cycpeptppb.
Supplementary information
Supplementary data are available at Bioinformatics online. |
|---|---|
| AbstractList | Abstract
Motivation
In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of a compound in drug discovery and design. However, due to structural differences, previous computational prediction methods developed for small-molecule compounds cannot be successfully applied to cyclic peptides, and methods for predicting the PPB rate of cyclic peptides with high accuracy are not yet available.
Results
Cyclic peptides are larger than small molecules, and their local structures have a considerable impact on PPB; thus, molecular descriptors expressing residue-level local features of cyclic peptides, instead of those expressing the entire molecule, as well as the circularity of the cyclic peptides should be considered. Therefore, we developed a prediction method named CycPeptPPB using deep learning that considers both factors. First, the macrocycle ring of cyclic peptides was decomposed residue by residue. The residue-based descriptors were arranged according to the sequence information of the cyclic peptide. Furthermore, the circular data augmentation method was used, and the circular convolution method CyclicConv was devised to express the cyclic structure. CycPeptPPB exhibited excellent performance, with mean absolute error (MAE) of 4.79% and correlation coefficient (R) of 0.92 for the public drug dataset, compared to the prediction performance of the existing PPB rate prediction software (MAE=15.08%, R=0.63).
Availability and implementation
The data underlying this article are available in the online supplementary material. The source code of CycPeptPPB is available at https://github.com/akiyamalab/cycpeptppb.
Supplementary information
Supplementary data are available at Bioinformatics online. In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of a compound in drug discovery and design. However, due to structural differences, previous computational prediction methods developed for small-molecule compounds cannot be successfully applied to cyclic peptides, and methods for predicting the PPB rate of cyclic peptides with high accuracy are not yet available. Cyclic peptides are larger than small molecules, and their local structures have a considerable impact on PPB; thus, molecular descriptors expressing residue-level local features of cyclic peptides, instead of those expressing the entire molecule, as well as the circularity of the cyclic peptides should be considered. Therefore, we developed a prediction method named CycPeptPPB using deep learning that considers both factors. First, the macrocycle ring of cyclic peptides was decomposed residue by residue. The residue-based descriptors were arranged according to the sequence information of the cyclic peptide. Furthermore, the circular data augmentation method was used, and the circular convolution method CyclicConv was devised to express the cyclic structure. CycPeptPPB exhibited excellent performance, with mean absolute error (MAE) of 4.79% and correlation coefficient (R) of 0.92 for the public drug dataset, compared to the prediction performance of the existing PPB rate prediction software (MAE=15.08%, R=0.63). The data underlying this article are available in the online supplementary material. The source code of CycPeptPPB is available at https://github.com/akiyamalab/cycpeptppb. Supplementary data are available at Bioinformatics online. In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of a compound in drug discovery and design. However, due to structural differences, previous computational prediction methods developed for small-molecule compounds cannot be successfully applied to cyclic peptides, and methods for predicting the PPB rate of cyclic peptides with high accuracy are not yet available.MOTIVATIONIn recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is a significant pharmacokinetic property of a compound in drug discovery and design. However, due to structural differences, previous computational prediction methods developed for small-molecule compounds cannot be successfully applied to cyclic peptides, and methods for predicting the PPB rate of cyclic peptides with high accuracy are not yet available.Cyclic peptides are larger than small molecules, and their local structures have a considerable impact on PPB; thus, molecular descriptors expressing residue-level local features of cyclic peptides, instead of those expressing the entire molecule, as well as the circularity of the cyclic peptides should be considered. Therefore, we developed a prediction method named CycPeptPPB using deep learning that considers both factors. First, the macrocycle ring of cyclic peptides was decomposed residue by residue. The residue-based descriptors were arranged according to the sequence information of the cyclic peptide. Furthermore, the circular data augmentation method was used, and the circular convolution method CyclicConv was devised to express the cyclic structure. CycPeptPPB exhibited excellent performance, with mean absolute error (MAE) of 4.79% and correlation coefficient (R) of 0.92 for the public drug dataset, compared to the prediction performance of the existing PPB rate prediction software (MAE=15.08%, R=0.63).RESULTSCyclic peptides are larger than small molecules, and their local structures have a considerable impact on PPB; thus, molecular descriptors expressing residue-level local features of cyclic peptides, instead of those expressing the entire molecule, as well as the circularity of the cyclic peptides should be considered. Therefore, we developed a prediction method named CycPeptPPB using deep learning that considers both factors. First, the macrocycle ring of cyclic peptides was decomposed residue by residue. The residue-based descriptors were arranged according to the sequence information of the cyclic peptide. Furthermore, the circular data augmentation method was used, and the circular convolution method CyclicConv was devised to express the cyclic structure. CycPeptPPB exhibited excellent performance, with mean absolute error (MAE) of 4.79% and correlation coefficient (R) of 0.92 for the public drug dataset, compared to the prediction performance of the existing PPB rate prediction software (MAE=15.08%, R=0.63).The data underlying this article are available in the online supplementary material. The source code of CycPeptPPB is available at https://github.com/akiyamalab/cycpeptppb.AVAILABILITY AND IMPLEMENTATIONThe data underlying this article are available in the online supplementary material. The source code of CycPeptPPB is available at https://github.com/akiyamalab/cycpeptppb.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. |
| Author | Yoshikawa, Yasushi Ohue, Masahito Yanagisawa, Keisuke Akiyama, Yutaka Li, Jianan |
| Author_xml | – sequence: 1 givenname: Jianan orcidid: 0000-0002-9004-5485 surname: Li fullname: Li, Jianan – sequence: 2 givenname: Keisuke orcidid: 0000-0003-0224-0035 surname: Yanagisawa fullname: Yanagisawa, Keisuke – sequence: 3 givenname: Yasushi surname: Yoshikawa fullname: Yoshikawa, Yasushi – sequence: 4 givenname: Masahito orcidid: 0000-0002-0120-1643 surname: Ohue fullname: Ohue, Masahito – sequence: 5 givenname: Yutaka orcidid: 0000-0003-2863-8703 surname: Akiyama fullname: Akiyama, Yutaka email: akiyama@c.titech.ac.jp |
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Motivation
In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be... In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by... |
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| SubjectTerms | Blood Proteins Deep Learning Original Papers Peptides, Cyclic Protein Binding Software |
| Title | Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning |
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