Jul 2026· Journal of Medicinal Chemistry· Vol 69, pp. 16234 - 16243· 0 citations· 34 references
Medicine
TL;DR
A comparative, structure-driven analysis of PD-L1 complexes deposited in the Protein Data Bank is presented and it is demonstrated that distinct inhibitory modalities converge on the same functional CC′FG hotspot region while employing fundamentally different neutralization mechanisms.
Abstract
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.
Fragment-based diffusion modeling is an efficient and interpretable strategy for the discovery of computationally prioritized PD-L1 small-molecule candidate inhibitors and offers a promising framework for tackling challenging targets in cancer immunotherapy.
Jun Liu, Yuxing Yi, Xiaoyan Wu et al.· Molecular diversity· 0 citations
The quaternary ammonium strategy represents an effective approach to developing water-soluble PD-1/PD-L1 inhibitors with dual immunomodulatory and antiangiogenic functions.
Jianwei Xu, Pan Yang, Xixiang Yang et al.· Journal of Medicinal Chemist...· 0 citations
Abstract Small-molecule stabilization of G-quadruplexes (G4s) has become an active focus in nucleic acid-targeted drug discovery. The mechanisms of the ligands’ binding selectivity and biological activities are critical for rational drug design. CX-5461, the first clinically advanced G4-targeting agent, has shown notable efficacy in DNA repair–deficient cancers. Its close analogue MTR-106 also displayed comparable anti-proliferative effects on cancer cells. However, the molecular basis of their interaction with G4s remains elusive. Here, through differential scanning calorimetry, complementary biophysical assays, and solution NMR technique, we probed their recognition modes with G4s. Although both ligands induced stronger thermal stabilization of the parallel G4s, the MYT1L quadruplex–duplex hybrid (QDH) formed the most homogeneous ligand-bound complexes in solution, highlighting the G4–duplex junction as a potential recognition site. Solution structural determination at high resolution demonstrated that both CX-5461 and MTR-106 inserted into the G4–duplex junction pocket. Their rigid polyaromatic scaffolds stacked with the 3′-end G-tetrad of G4, while their flexible side chains extended into the groove of QDH to enable spatial recognition. These findings elucidated the molecular basis of G4 recognition by CX-5461 and MTR-106, and provided a structural framework for the rational development of next-generation G4-targeted therapeutics with improved selectivity and efficacy.
Yubo Li, Kefu Liu, Xiaodong Hu et al.· Nucleic Acids Research· 1 citation
AlphaFold 3 (AF3) and Boltz-2 are state-of-the-art AI-based tools for biomolecular structure prediction, but whether their predictions provide useful guidance for lead optimization, SAR interpretation, and virtual screening remains insufficiently characterized. We benchmarked their performance using newly determined soluble epoxide hydrolase co-crystal structures and matched activity data together with a curated post-training-cutoff dataset spanning kinases, allosteric modulators, covalent systems, PROTACs, molecular glues, fragments, membrane proteins, RNA binders, and activity-cliff pairs. Both models recovered canonical orthosteric enzyme and kinase complexes, including key DFG/αC conformational states, whereas allosteric, membrane-protein, and induced-proximity complexes remained challenging. Pharmacophore RMSD was often lower than overall ligand RMSD, indicating preservation of key recognition features despite imperfect whole-ligand alignment. AF3 minPAE correlated with pose accuracy, and very low minPAE values (<0.85 Å) were strongly enriched for accurate poses. Model confidence scores were not associated with experimental activity, whereas Boltz-2 predicted affinity captured relative activity trends and distinguished the activity-cliff pair, although its performance varied across ligand series.
Ke Chen, Zuo-Huang Qi, Omar Lozano Ramos et al.· bioRxiv· 0 citations
Mediation of protein–protein interactions with molecules that bind strongly and selectively to one of the partners at the protein interface is a promising therapeutic strategy for myriad diseases. One such approach is the rational design of non-peptidic scaffolds that reproduce the display of amino acid side chains from one face of a secondary structural element. We have previously disclosed proof-of principle syntheses of β-strand mimetics composed of alternating (hetero)aromatic and cyclic urea units, conformationally preorganised through dipolar repulsion in organic solvents, that are in good agreement with the i, i + 2, and i + 4 side-chain vectors of a canonical strand. Here we demonstrate sequence diversity of the approach through the incorporation of hydrophobic and hydrophilic side-chain mimics via an improved synthetic route. The scaffold is conformationally preorganised for target binding in aqueous media including buffer, is readily soluble, and thus is suitable for elaboration and deployment against specific protein targets.
R. Bannister, Emily F Jones, Jonathan E Ross et al.· Organic and biomolecular che...· 0 citations
The development of theranostic tools for the early detection and localization of tumors represents a major challenge in oncology. Among emerging strategies, the targeting of Programmed Death Ligand-1 (PD-L1), a key immune checkpoint protein overexpressed in many tumor types, has gained significant attention. In this work, we report design and development of theranostic gold nanostructures functionalized with PD-L1-targeting peptides (PTP, sPTP, and rPTP) whose sequences were identified combining structural analysis of the PD-1/PD-L1 interaction interface and molecular dynamics simulations. This is because the design of functional nanostructures for protein targeting requires a precise understanding of how molecular recognition is affected by ligand organization at interfaces; therefore, peptide design was guided not only by the selection of key residues involved in binding but also by the evaluation of peptide assemblies to explicitly account for the collective effects governing target recognition. Indeed, beyond conventional evaluation of protein/single-peptide interaction, peptide clusters and surface-anchored monolayers were investigated to consider features like peptide assembly, organization, and reduced conformational freedom in the nanostructure/PD-L1 interaction. Results indicate that peptide sequence and orientation critically determine monolayer organization and accessibility of the PD-L1 binding motif. The computational predictions were experimentally validated by synthesizing peptide-functionalized gold nanostructures and evaluating their targeting performance against MDA-MB-231 breast cancer cells over-expressing PD-L1, using the surface-enhanced Raman scattering technique: NS functionalized with PTPs achieved the targeting of approximately 85% of MDA-MB-231 cells at 100 pM nanostructure concentration, compared to 23% for those functionalized with rPTP, demonstrating a nearly four-fold difference attributable exclusively to peptide orientation on the nanostructure surface. The specific system investigated in this work establishes a computational framework for the rational design of peptide-functionalized nanostructures, providing insights into the collective behavior of peptide monolayers and offering a smart methodology that, while demonstrated here for targeting PD-L1, is in principle applicable to other protein targets.
Micaela Giannetti, Marina Gobbo, Lucio Litti et al.· ACS Applied Bio Materials· 0 citations