Title:
METHOD FOR PREDICTING CELL MEMBRANE PERMEABILITY OF CYCLIC PEPTIDE
Document Type and Number:
WIPO Patent Application WO/2024/043251
Kind Code:
A1
Abstract:
The present invention addresses the problem of providing a method for predicting the cell membrane permeability of a cyclic peptide that enables the versatile design of cell membrane permeable cyclic peptides. The present invention provides a method for predicting the cell membrane permeability of a cyclic peptide, wherein the prediction method comprises: a first step that acquires the structure of a cyclic peptide; a second step that calculates a molecular shape factor r calculated by formula (1) via a stage that performs ellipsoidal approximation to determine each axis length of a, b, and c, when the axial length in the longest axial direction of the main chain structure in the structure acquired in the first step is taken as a and the axial lengths of the other two directions that are orthogonal to a and orthogonal to each other are taken as b and c; and a third step that assesses that the cyclic peptide is cell membrane permeable if the molecular shape factor r is in the range of 0.4-0.6.
Inventors:
TAMURA TAKASHI (JP)
KANEKO MAI (JP)
YOSHIMITSU YUJI (JP)
TSUMURA KYOSUKE (JP)
SUZUKI KOO (JP)
OHASHI NORIYUKI (JP)
HASHIMOTO ICHIHIKO (JP)
MIYAHARA KENTA (JP)
KOCHI MASAHIRO (JP)
HORIGOME HIROKI (JP)
KANEKO MAI (JP)
YOSHIMITSU YUJI (JP)
TSUMURA KYOSUKE (JP)
SUZUKI KOO (JP)
OHASHI NORIYUKI (JP)
HASHIMOTO ICHIHIKO (JP)
MIYAHARA KENTA (JP)
KOCHI MASAHIRO (JP)
HORIGOME HIROKI (JP)
Application Number:
PCT/JP2023/030224
Publication Date:
February 29, 2024
Filing Date:
August 23, 2023
Export Citation:
Assignee:
FUJIFILM CORP (JP)
International Classes:
C07K2/00
Domestic Patent References:
| WO2021141684A1 | 2021-07-15 |
Foreign References:
| JP2022131959A | 2022-09-07 | |||
| JP2015042159A | 2015-03-05 |
Other References:
YAMADA YUTA, YOSHIKAWA YASUSHI, WAKUI NAOKI, OHUE MASAHITO, AKIYAMA YUTAKA: "Developement of membrane permeability prediction method for cyclic peptides with machine learning", IPSJ SIG TECHNICAL REPORT, vol. 2019-BIO-57, no. 13, 9 March 2019 (2019-03-09), pages 1 - 8, XP093144652, ISSN: 2188-8590
PARTRIDGE ANTHONY W., KAAN HUNG YI KRISTAL, JUANG YU-CHI, SADRUDDIN AHMAD, LIM SHUHUI, BROWN CHRISTOPHER J., NG SIMON, THEAN DAWN,: "Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties", MOLECULES, MDPI AG, CH, vol. 24, no. 12, 20 June 2019 (2019-06-20), CH , pages 2292, XP093142680, ISSN: 1420-3049, DOI: 10.3390/molecules24122292
LAWRENCE NICOLE, PHILIPPE GRÉGOIRE J.-B., HARVEY PETA J., CONDON NICHOLAS D., BENFIELD AURÉLIE H., CHENEVAL OLIVIER, CRAIK DAVID J: "Cyclic peptide scaffold with ability to stabilize and deliver a helical cell-impermeable cargo across membranes of cultured cancer cells", RSC CHEMICAL BIOLOGY, THE ROYAL SOCIETY OF CHEMISTRY, vol. 1, no. 5, 8 December 2020 (2020-12-08), pages 405 - 420, XP093142681, ISSN: 2633-0679, DOI: 10.1039/D0CB00099J
WANG YENG-TSENG, CHENG TIAN-LU: "Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations", JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, ADENINE PRESS, NEW YORK, NY, US, vol. 39, no. 11, 24 July 2021 (2021-07-24), US , pages 4005 - 4014, XP093144654, ISSN: 0739-1102, DOI: 10.1080/07391102.2020.1773317
PARTRIDGE ANTHONY W., KAAN HUNG YI KRISTAL, JUANG YU-CHI, SADRUDDIN AHMAD, LIM SHUHUI, BROWN CHRISTOPHER J., NG SIMON, THEAN DAWN,: "Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties", MOLECULES, MDPI AG, CH, vol. 24, no. 12, 20 June 2019 (2019-06-20), CH , pages 2292, XP093142680, ISSN: 1420-3049, DOI: 10.3390/molecules24122292
LAWRENCE NICOLE, PHILIPPE GRÉGOIRE J.-B., HARVEY PETA J., CONDON NICHOLAS D., BENFIELD AURÉLIE H., CHENEVAL OLIVIER, CRAIK DAVID J: "Cyclic peptide scaffold with ability to stabilize and deliver a helical cell-impermeable cargo across membranes of cultured cancer cells", RSC CHEMICAL BIOLOGY, THE ROYAL SOCIETY OF CHEMISTRY, vol. 1, no. 5, 8 December 2020 (2020-12-08), pages 405 - 420, XP093142681, ISSN: 2633-0679, DOI: 10.1039/D0CB00099J
WANG YENG-TSENG, CHENG TIAN-LU: "Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations", JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, ADENINE PRESS, NEW YORK, NY, US, vol. 39, no. 11, 24 July 2021 (2021-07-24), US , pages 4005 - 4014, XP093144654, ISSN: 0739-1102, DOI: 10.1080/07391102.2020.1773317
Attorney, Agent or Firm:
SIKS & CO. (JP)
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