Discovery and Crystallographic Study of Water-Soluble Quaternary Ammonium-Based PD-1/PD-L1 Inhibitors with Anti-Angiogenic Activity

Fragment-based diffusion modeling and molecular dynamics simulation validation for the discovery of PD-L1 small-molecule inhibitors.

Novel Selenium-Containing Small Molecule PD-L1 Inhibitors: Design, Synthesis, and Evaluation of the Antitumor Activity.

Novel selenium-containing small molecule PD-L1 inhibitors were designed and synthesized for the first time to explore their potential as antitumor agents. By computer-aided structural optimization, HTRF and SPR techniques, compound SA13 was identified as the most potent blocker of the PD-1/PD-L1 interaction, exhibiting an IC50 value of 5.2 ± 0.5 nM, a KD value of 9.06 ± 1.25 nM, respectively. Study on the SA13/hPD-L1 cocrystal structure (2.9 Å) revealed a unique selenomethyl-involved binding mode, which may interpret its superior inhibitory activity compared to other analogs. Cell-based assays showed that SA13 can mediate the internalization of PD-L1 and strongly block hPD-1 and hPD-L1 interaction, demonstrating its effectiveness in biological events. Notably, in the Hu-PD-L1 MC38 mouse model, SA13 significantly inhibited tumor growth, with a tumor growth inhibition (TGI) rate of 77.79% (60 mg/kg, administrated intragastrically) with no observable toxicity. These data indicate that SA13 is a promising and safe novel antitumor agent worthy of further development.

3-amino-1,2,4-triazine scaffolds as next-generation PDK inhibitors: Design, mechanistic insights, and efficacy in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer characterized by late diagnosis, aggressiveness, metabolic plasticity, and resistance to therapy, underscoring the need for new molecular targets. Pyruvate dehydrogenase kinases (PDKs), particularly PDK1 and PDK4, drive metabolic reprogramming and tumor progression, making them attractive therapeutic targets. However, current PDK inhibitors show limited potency and selectivity. Recent 3-amino-1,2,4-triazine derivatives have demonstrated promising PDK1/PDK4 inhibition and antiproliferative activity in PDAC cells, leading to the design of a new library of sixty triazine compounds, here in reported. Several compounds exhibited strong inhibitory activity against PDK1 and PDK4, with IC50 values ranging from 0.06 to 1.1 μM, demonstrating markedly higher potency compared to DCA and pronounced isoform selectivity. Molecular modeling and supervised molecular dynamics simulations supported these findings, revealing stable binding of representative compounds within the nucleotide-binding pocket of PDK1, involving key interactions with Asp318, Arg286, and Lys327. Functionally, the compounds displayed potent antiproliferative activity in both KRAS wild-type and mutant PDAC cell lines, with micromolar IC50 values. In three-dimensional pancreatic cancer spheroid models, the most active derivatives outperformed gemcitabine by approximately threefold and exceeded the activity of DCA-derived PDK inhibitors by ∼1.7-fold. Mechanistically, the novel amino-triazines disrupted the PDK/PDH axis, inducing a metabolic shift toward oxidative phosphorylation, impairing mitochondrial function, and triggering apoptotic cell death in KRAS-mutant PSN-1 cells. Overall, these results identify amino-triazine-based scaffolds as a promising new class of potent and selective PDK inhibitors with significant anticancer potential in pancreatic cancer.

One Face, Three Solutions: Structural Convergence in PD-L1 Inhibition across Antibodies, Macrocycles, and Small Molecules

Protein–protein interactions dominated by large, flat interfaces are widely considered challenging drug targets. The programmed cell death protein-1/programmed death ligand-1 (PD-1/PD-L1) immune checkpoint exemplifies this problem, as the interaction is mediated by an extended β-sheet surface lacking deep pockets. Despite this, PD-L1 has been successfully inhibited by chemically distinct modalities, including antibodies, macrocyclic peptides, and small molecules. Here, we present a comparative, structure-driven analysis of PD-L1 complexes deposited in the Protein Data Bank and demonstrate a striking convergence: all effective inhibitors engage the same CC′FG β-sheet face of PD-L1. Antibodies directly occlude this surface, macrocyclic peptides such as pAC65 reproduce antibody-like surface coverage in a compact and preorganized scaffold, and biphenyl small molecules neutralize the same epitope indirectly by inducing PD-L1 homodimerization. This unified structural framework reveals modality-agnostic design principles for targeting flat immune checkpoint PPIs. This Perspective provides a unified structural framework for understanding PD-L1 inhibition across clinically tested antibodies, macrocyclic peptides, and small molecules. Both visualizing and quantitatively comparing interface overlap, hotspot conservation, and buried surface area, the work demonstrates that distinct inhibitory modalities converge on the same functional CC′FG hotspot region while employing fundamentally different neutralization mechanisms. These findings establish structure-guided principles for the rational design of next-generation PD-L1 modulators across diverse therapeutic modalities.

Dual-targeting CD73/PD-L1 bifunctional inhibitor: a promising cancer immunotherapy strategy

Objectives This work aims to design and characterize a novel bifunctional small molecule that simultaneously targets PD-L1 and CD73 to enhance the therapeutic efficacy of tumor immunotherapy. Methods Multiple methodologies were integrated for compound screening and biological characterization, including computer-aided molecular docking, homogeneous time-resolved fluorescence (HTRF) binding assay, surface plasmon resonance (SPR), and PD-1/PD-L1 NFAT reporter cell assay. Results The lead compound CP-1 exhibited potent dual-target inhibitory activities. It blocked the PD-1/PD-L1 interaction with an IC50 of 10.27 nM and suppressed CD73 activity with an IC50 of 300.2 nM. Molecular docking simulations revealed that CP-1 stably binds to the functional domains of PD-L1 and CD73 via specific non-covalent interactions. Cellular functional assays further demonstrated that CP-1 effectively restored T cell function in the PD-1/PD-L1 reporter system, with an EC50 of 0.9 μM. Conclusions CP-1 exhibits balanced, dual-nanomolar inhibitory activity against PD-L1 and CD73 and displays potent immunomodulatory effects at the cellular level. It serves as a promising lead candidate for developing novel bifunctional agents to advance tumor immunotherapy.

Structure-Based Design and Evaluation of Coumarin-Derived CDK4 Inhibitors for Non-Small Cell Lung Cancer: An Integrated Computational Study.