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

Abstract

PD-1/PD-L1 protein complex is attracting a great deal of interest as a drug target for the design of immune therapies able to block its assembly. Although some biologic drugs have entered clinical use, their poor response rate in patients are demanding further efforts to design small molecule inhibitors of PD-1/PD-L1 complex with higher efficacy and optimal physicochemical properties. Dysregulation of pH in the tumor microenvironment is indeed one of the key mechanisms promoting drug resistance and lack of response in cancer therapy. Integrating computational and biophysical approaches, herein we report a screening campaign that has led to identifying VIS310 as a novel ligand of PD-L1, with physicochemical properties enabling a pH-dependent binding potency. Additional optimization efforts by analogue-based screening have been instrumental to disclosing VIS1201, which exhibits improved binding potency against PD-L1 and is able to inhibit PD-1/PD-L1 complex formation in a ligand binding displacement assay. While providing preliminary structure–activity relationships (SARs) of a novel class of PD-L1 ligands, our results lay the foundation for the discovery of immunoregulatory small molecules resilient to tumor microenvironmental conditions for escaping drug-resistance mechanisms.

A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules

“…The most active compound, VIS310 ( Figure 9 ), showed a high-micromolar dissociation constant (Kd = 163.75 ± 33.61 μM), and better binding efficiency index (BEI = 21.0) than BMS-202 (Kd = 8.13 ± 1.38 μM; BEI = 12.1). Since VIS310 was the only substituted benzamidoxime of the analyzed database, the analogue-based approach to screen the REAL database of Enamine, containing about 43.8 million drug-like compounds, was used to define the structure-activity relationships of benzamidoxime compounds [ 91 ].…”