26RW

Crystal structure of the C65A/M94W/M145W/C167A mutant of Human lipocalin-type Prostaglandin D Synthase in complex with 10-O-(3-fluoropropyl)-substituted SN-38

This is a non-PDB format compatible entry.

Summary for 26RW

• Entry DOI: 10.2210/pdb26rw/pdb
• Descriptor: Prostaglandin-H2 D-isomerase, (4S)-4,11-diethyl-9-(3-fluoropropoxy)-4-hydroxy-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinoline-3,14(4H,12H)-dione (3 entities in total)
• Functional Keywords: lipocalin family, beta barrel structure, hydrophobic drug, drug delivery system, isomerase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 19811.97

Authors

Muroya, H.,Nishimura, S.,Inui, T. (deposition date: 2026-05-12, release date: 2026-09-16)

Primary citation

Nakatsuji, M.,Muroya, H.,Okubo, R.,Teraoka, Y.,Yamada, M.,Nishide, K.,Yoshida, H.,Furuta, K.,Koyama, R.,Kida, T.,Doi, H.,Nishimura, S.,Inui, T.
Development of a drug delivery vehicle protein exhibiting high binding affinity and low leakage of the anti-cancer drug SN-38.
Int.J.Biol.Macromol., 381:154313-154313, 2026

PubMed Abstract: Drug leakage from delivery vehicles is a major limitation of drug delivery systems (DDSs) for cancer chemotherapy because premature release of loaded drugs reduces therapeutic efficacy and increases off-target toxicity. We previously developed a DDS for the poorly water-soluble anti-cancer drug SN-38 using lipocalin-type prostaglandin D synthase (L-PGDS). To suppress drug leakage, in this study we generated an L-PGDS mutant (M94W-M145W) with enhanced binding affinity for SN-38 by introducing amino acid substitutions into the ligand-binding cavity. Docking simulations identified residues involved in SN-38 recognition, and selected residues were replaced with tryptophan to strengthen ligand binding. The dissociation constant of the M94W-M145W mutant for SN-38 was 2.7 ± 0.4 μM, approximately 4-fold lower than that of L-PGDS. In addition, 1 mM M94W-M145W enhanced the solubility of SN-38 by approximately 3.3-fold compared with 1 mM L-PGDS. In vitro release assays showed that the SN-38/M94W-M145W complex released SN-38 more slowly than the SN-38/L-PGDS complex. We also determined the crystal structure of the 10-O-(3-fluoropropyl)-substituted SN-38 derivative/M94W-M145W complex. The overall structure of M94W-M145W retained the typical lipocalin fold, indicating that these substitutions do not alter the global protein architecture. Two SN-38 derivative molecules were accommodated within the cavity through hydrogen bonding and hydrophobic interactions, including π-π stacking interactions introduced by the substituted tryptophan residues. These findings demonstrate that simple amino acid substitutions in L-PGDS can optimize drug binding, improve solubility, and suppress drug release, thus providing a basis for affinity-driven design of protein-based DDSs.

PubMed: 42680028
DOI: 10.1016/j.ijbiomac.2026.154313

Experimental method

X-RAY DIFFRACTION (1.24 Å)