9ERY image
Entry Detail
PDB ID:
9ERY
Keywords:
Title:
Co-crystal strucutre of PD-L1 with low molecular weight inhibitor
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-03-25
Release Date:
2024-07-24
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.27
R-Value Work:
0.22
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Programmed cell death 1 ligand 1
Chain IDs:A, B
Chain Length:131
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Design, synthesis, and evaluation of antitumor activity of 2-arylmethoxy-4-(2-fluoromethyl-biphenyl-3-ylmethoxy) benzylamine derivatives as PD-1/PD-l1 inhibitors.
Eur.J.Med.Chem. 276 116683 116683 (2024)
PMID: 39032403 DOI: 10.1016/j.ejmech.2024.116683

Abstact

A series of novel 2-arylmethoxy-4-(2-fluoromethyl-biphenyl-3-ylmethoxy) benzylamine derivatives was designed, synthesized, and evaluated for their antitumor effects as PD-1/PD-L1 inhibitors both in vitro and in vivo. Firstly, the ability of these compounds to block the PD-1/PD-L1 immune checkpoint was assessed using the homogeneous time-resolved fluorescence (HTRF) assay. Two of the compounds can strongly block the PD-1/PD-L1 interaction, with IC50 values of less than 10 nM, notably, compound HD10 exhibited significant clinical potential by inhibiting the PD-1/PD-L1 interaction with an IC50 value of 3.1 nM. Further microscale thermophoresis (MST) analysis demonstrated that HD10 had strong interaction with PD-L1 protein. Co-crystal structure (2.7 Å) analysis of HD10 in complex with the PD-L1 protein revealed a strong affinity between the compound and the target PD-L1 dimer. This provides a solid theoretical basis for further in vitro and in vivo studies. Next, a typical cell-based experiment demonstrated that HD10 could remarkably prevent the interaction of hPD-1 293 T cells from human recombinant PD-L1 protein, effectively restoring T cell function, and promoting IFN-γ secretion in a dose-dependent manner. Moreover, HD10 was effective in suppressing tumor growth (TGI = 57.31 %) in a PD-1/PD-L1 humanized mouse model without obvious toxicity. Flow cytometry, qPCR, and immunohistochemistry data suggested that HD10 inhibits tumor growth by activating the immune system in vivo. Based on these results, it seems likely that HD10 is a promising clinical candidate that should be further investigated.

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