9LJ3 image
Deposition Date 2025-01-14
Release Date 2025-06-25
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9LJ3
Keywords:
Title:
Crystal structure of P25
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.15 Å
R-Value Free:
0.28
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Programmed cell death 1 ligand 1
Gene (Uniprot):CD274
Chain IDs:A (auth: B), B (auth: A), C, D, E, F
Chain Length:123
Number of Molecules:6
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Discovery and Crystallography Study of Novel Resorcinol Dibenzyl Ether-Based PD-1/PD-L1 Inhibitors with Improved Drug-like and Pharmacokinetic Properties for Cancer Treatment.
J.Med.Chem. 68 12593 12614 (2025)
PMID: 40518797 DOI: 10.1021/acs.jmedchem.5c00344

Abstact

Current studies on PD-1/PD-L1 small-molecule inhibitors mainly focus on modifying the linker region between the biphenyl ring and amino acid side chains, or transforming the biphenyl ring into a benzodioxane structure. Herein, we designed and synthesized a series of compounds by introducing a tail at the terminal phenyl ring as small-molecule PD-1/PD-L1 inhibitors. Among them, compound NPH16 exhibited the most potent PD-L1 inhibitory activity (IC50 = 24.4 nM). The X-ray crystal structure further confirmed the high binding affinity of NPH16 to PD-L1 dimer. In the HepG2/Jurkat T cell coculture model, NPH16 promoted HepG2 cell apoptosis dose-dependently. In addition, NPH16 showed excellent in vivo antitumor efficacy (TGI = 92.1%) in a Hepa1-6 mouse tumor model and increased CD8+ cells in tumor microenvironment. Importantly, NPH16 possessed favorable pharmacokinetic properties with an oral bioavailability of 15.9%. Collectively, compound NPH16 represents a promising PD-1/PD-L1 inhibitor worthy of further investigation as a potential anticancer agent.

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Primary Citation of related structures