The Stone Guest: How Does pH Affect Binding Properties of PD‐1/PD‐L1 Inhibitors?

Abstract

The interaction between programmed cell death‐1 (PD‐1) and its ligand PD−L1 activates a coinhibitory signal that blocks T‐cell activation, promoting the immune escape process in the tumor microenvironment. Development of monoclonal antibodies targeting and inhibiting PD‐1/PD−L1 interaction as anticancer immunotherapies has proved successful in multiple clinical settings and for various types of cancer. Notwithstanding, limitations exist with the use of these biologics, including drug resistance and narrow therapeutic response rate in a majority of patients, that demand for the design of more efficacious small molecule‐based immunotherapies. Alteration of pH in the tumor microenvironment is a key factor that is involved in promoting drug resistance, tumor survival and progression. In this study, we have investigated the effect of pH shifts on binding properties of distinct classes of PD−L1 inhibitors, including macrocyclic peptide and small molecules. Results expand structure‐activity relationships of PD−L1 inhibitors, providing insights into structural features and physicochemical properties that are useful for the design of ligands that may escape a drug resistance mechanism associated to variable pH conditions of tumor microenvironment.

Turning a Tumor Microenvironment Pitfall into Opportunity: Discovery of Benzamidoxime as PD-L1 Ligand with pH-Dependent Potency

“…We previously reported that the binding activity of BMS-202 ( 5 ) is affected by the pH condition of the experiment, with lower pH values strengthening its interaction with PD-L1 (pH 6.2; K d = 4.50 ± 0.56 μM; BEI = 12.8) [ 27 ]. Accordingly, a second binding experiment of VIS310 was carried out against PD-L1 at pH 6.2, resulting in a significant improvement of the ligand binding activity (pH 6.2, K d = 47.81 ± 11.50 μM; BEI = 24.0; Figure 4 ).…”

“…In a previous study, we found that alterations of pH, as those occurring in the tumor microenvironment, affect the strength of ligand binding to PD-L1 [ 27 ]. That study highlighted the relevance of electrostatic force in ligand/protein interactions of PD-1/PD-L1 inhibitors.…”

“…The aim of the structure-based screening campaign was the identification of small molecules with pH-dependent binding activity to PD-L1. To achieve this goal, a virtual library of small molecules was docked into a binding site of PD-L1 defined around the residues Asp122 and Lys124 ( Figure 2 ), which were identified as key residues (hot-spots) for ligand recognition in a previous work [ 27 ].…”

“…The wide hydrophobic and shallow surface of the binding site is a challenging aspect for designing drug-like inhibitors of the PD-1/PD-L1 interaction for clinical development. More recently, we have shown that pH shifts, as those occurring in the tumor microenvironment upon lactic acid production [ 25 , 26 ], represent a further obstacle, affecting the binding properties of PD-L1 ligands [ 27 ].…”

Solubilizer tag effect on PD-L1/inhibitor binding properties for m-terphenyl derivatives

“…The general observation based on the docking results is that the positive charge generated on the protonated amine in the solubilizer tag corresponds to a higherscoring function result compared to the neutral form of the ligand. This is related to the N + -H … B Asp122 salt bridge formation that has a strong positive in uence on the protein-ligand complex stabilization due to its strength (Riccio et al, 2021).…”