BMS-1166 (PD-1/PD-L1-IN1)

Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells

Antibodies targeting the PD-1/PD-L1 immune checkpoint achieved spectacular success in anticancer therapy in the recent years. In contrast, no small molecules with cellular activity have been reported so far. Here we provide evidence that small molecules are capable of alleviating the PD-1/PD-L1 immune checkpoint-mediated exhaustion of Jurkat T-lymphocytes. The two optimized small-molecule inhibitors of the PD-1/PD-L1 interaction, BMS-1001 and BMS-1166, developed by Bristol-Myers Squibb, bind to human PD-L1 and block its interaction with PD-1, when tested on isolated proteins. The compounds present low toxicity towards tested cell lines and block the interaction of soluble PD-L1 with the cell surface-expressed PD-1. As a result, BMS-1001 and BMS-1166 alleviate the inhibitory effect of the soluble PD-L1 on the T-cell receptor-mediated activation of T-lymphocytes. Moreover, the compounds were effective in attenuating the inhibitory effect of the cell surface-associated PD-L1. We also determined the X-ray structures of the complexes of BMS-1001 and BMS-1166 with PD-L1, which revealed features that may be responsible for increased potency of the compounds compared to their predecessors. Further development may lead to the design of an anticancer therapy based on the orally delivered immune checkpoint inhibition.

Targeting cryptic-orthosteric site of PD-L1 for inhibitor identification using structure-guided approach

Approved mAbs that block the protein-protein interaction (PPI) interface of the PD-1/PD-L1 immune checkpoint axis have led to significant improvements in cancer treatment. Despite having drawbacks of mAbs only few a compounds are reported till date against this axis. Inhibiting PPIs using small molecules has emerged as a significant therapeutic opportunity, demanding for the identification of drug-like molecules at an accelerated pace under the hit-to-lead campaigns. Due to the PD-L1's cross-talk with PD-1/CD80 and its overexpression on cancer cells, as well as the availability of its crystal structures with small molecules, it is an enticing therapeutic target for structure-assisted small molecule design. Furthermore, the selection of chemical databases enriched with focused designing for PPI interfaces is crucial. Therefore, in this study we have utilized the Asinex signature library for structure-assisted virtual screening to find the potential PD-L1 inhibitors by targeting the cryptic PD-L1 interface, followed by induced fit docking for pose refinements in the pocket. The obtained hits were then subjected to interaction fingerprinting and ligand-based drug-likeness investigations in order to evaluate and analyze their drug-like qualities (ADME). Twelve compounds qualified for molecular dynamics simulations, followed by thermodynamic calculations for evaluation of their stability and energetics inside the pocket. Two novel compounds with different chemical moieties have been identified that are consistent throughout the simulation, mimicking the interactions and binding energies with BMS-1166. These compounds appear as potential therapeutic candidates to be explored experimentally, thereby paving the way for the development of novel leads as immunomodulators.

Flurbiprofen as a biphenyl scaffold for the design of small molecules binding to PD-L1 protein dimer

Small molecules targeting the PD-1/PD-L1 immune checkpoint are actively searched to offer anticancer oral treatment modalities. Different small molecules have been designed, such as BMS-202 and BMS-1166 which potently bind to PD-L1, sequestering the protein dimer and thus preventing cancer cells to escape antitumor immune responses. A (top → down) deconvolution of BMS compounds has characterized their central biphenyl unit as the minimal element required for PD-L1 protein binding. On this basis, we searched for approved drugs containing a similar biphenyl unit and endowed with immune modulatory activities. We identified the biphenyl anti-inflammatory drug flurbiprofen (FLB) as a potential candidate for PD-L1 interaction, and then proposed a (bottom → up) convolution to select similar molecules, used in Human, susceptible to engage stable interactions with PD-L1. The hypothesis was tested by molecular modeling using the crystal structure of BMS-202 bound to the PD-L1 dimer. The calculations suggest that both (R) and (S) isomers of FLB can form stable complexes with PD-L1, penetrating deep into the cylindric pocket at the interface of the protein dimer. However, the potential energy of interaction (ΔE) is reduced by ~40% for FLB compared to BMS compounds. Then, we identified three FLB analogues (diflunisal, CHF-5074 and HCT1026) forming stable complexes with PD-L1. The longer FLB derivative HCT1026 appears as a suitable binder of the PD-L1 dimer, sliding well along the BMS binding cavity. Our approach proposes a new strategy to discover PD-L1-binding small molecules and raises the intriguing possibility that FLB can bind transiently to PD-L1, thus possibly explaining some of its biological effects. Our study opens new perspectives for the use of FLB (and analogs) as an immune modulator in oncology and other therapeutic domains.

Pharmacophore model of immunocheckpoint protein PD-L1 by cosolvent molecular dynamics simulations

Due to the clinical success of cancer immunotherapy, the design of PD-1/PD-L1 inhibitors has become an area of active research. To date, only five monoclonal antibodies are approved by FDA. Despite the great effort for the development of small molecules and peptides as inhibitors, only one of those has reached clinical trials. Pharmacophore models are a proven useful tool for drug design. The effectiveness of receptor-based pharmacophore modeling is limited due to the neglect of protein flexibility and desolvation effects. In the present application, we performed co-solvent molecular dynamics simulations of PD-L1 protein in order to obtain a pharmacophore model of PD-L1 immunecheckpoint protein. The analysis of probe molecules affinities by PD-L1 resulted in the identification of C'CFG beta strands as the zone with the highest convergence of hotspots, which corresponds to PD-1/PD-L1 interaction surface. The interactions maintained with PD-L1 residues varied from hydrophobic interactions to hydrogen bonds and salt bridges with critical residues for PD-1/PD-L1 binding (M115, A121, Y123, I54, Y56, E58, R125). The superposition of known inhibitors of PD-L1 as Peptide-57, BMS-1166 and high affinity PD-1(HAPD-1) allowed us to validate the pharmacophore model due to the good correlation with its features. The pharmacophore described herein can lead to the optimization and design of more selective and potent anti-cancer drugs.