Using PD-L1 full-length structure, enhanced induced fit docking and molecular dynamics simulations for structural insights into inhibition of PD-1/PD-L1 interaction by small-molecule ligands

The programmed cell death ligand protein 1 (PD-L1) is a strong immunosuppressive molecule that inactivates tumor-specific T cells by binding to the programmed cell death- 1 protein (PD-1). Cancer immunotherapy based on the monoclonal antibodies targeting the PD-1/PD-L1 pathway has demonstrated therapeutic responses without precedent over a wide range of cancers. However, the antibody-based immunotherapies have several limitations such as high production cost or the induction of severe immune-related adverse effects. Small-molecule inhibitors of the PD-1/PD-L1 pathway are a promising alternative or complementary therapeutic to antibodies. Currently, the field of developing anti-PD-1/PD-L1 small-molecule inhibitors is intensively explored. In the present study a pharmacophore model was generated based on previously developed compounds and their atomistic structures with the PD-L1 dimer. Structure-based affinity-based virtual screening of small-molecule inhibitors of the PD-1/PD-L1 pathway according to the pharmacophore model followed by a screening in terms of drug-likeness resulted in ten hit compounds of high affinity towards the PD-L1 dimer and the satisfaction to all of the drug-likeness rules. Molecular dynamics (MD) simulations showed that nine of ten compounds formed stable complexes with the PD-L1 dimer as evidenced by the analysis of MD trajectories. Molecular mechanics Poisson- Boltzmann surface area (MM-PBSA) calculation revealed very low binding energies (<-46 kcal/mol) for the interactions of these ligands with the PD-L1 dimer, suggesting that identified compounds may serve as good scaffolds for the design of novel agents of antitumor immunotherapy able to target the PD-1/PD-L1 interaction Communicated by Ramaswamy H. Sarma

T-cell activation through the blockade of PD-1 – PD-L1 interactions is recognised at present as one of the most promising strategies in the cancer treatment and a number of antibodies targeting the PD-1 – PD-L1 immune checkpoint pathway have been approved after successful clinical trials. However, the use of antibodies suffers from a number of shortcomings including poor tissue and tumor penetration, long half-life time, poor oral bioavailability, and expensive production costs. Small molecule based therapeutic approaches offer the potential to address the shortcomings of the antibody-based checkpoint inhibitors. At present, more than twenty small molecular inhibitors of the PD-1 – PD-L1 interactions whose scaffold is based on substituted biphenyl group connected to a further aromatic ring through a benzyl ether bond have been identified and patented by Bristol – Mayers – Squibb (USA). Structural studies have shown that all these compounds act by inducing the dimerisation of PD-L1 that makes PD-L1 non-competent for forming complex with PD-1. Very recently, the dietary polyphenol resveratrol (RSV) has been reported to inhibit the PD-1 – PD-L1 interactions through the induction of the PD-L1 dimerisation but the mechanisms remain unclear. Here, computational structural biology tools combining protein – protein and protein – ligand docking with molecular dynamics simulations were used to gain structural insights into the mechanisms of the RSV-induced dimerisation of PD-L1.

Recently, small-molecule compounds have been reported to block the PD-1/PD-L1 interaction by inducing the dimerization of PD-L1. All these inhibitors had a common scaffold and interacted with the cavity formed by two PD-L1 monomers. This special interactive mode provided clues for the structure-based drug design, however, also showed limitations for the discovery of small-molecule inhibitors with new scaffolds. In this study, we revealed the structure-activity relationship of the current small-molecule inhibitors targeting dimerization of PD-L1 by predicting their binding and unbinding mechanism via conventional molecular dynamics and metadynamics simulation. During the binding process, the representative inhibitors (BMS-8 and BMS-1166) tended to have a more stable binding mode with one PD-L1 monomer than the other and the small-molecule inducing PD-L1 dimerization was further stabilized by the non-polar interaction of Ile54, Tyr56, Met115, Ala121, and Tyr123 on both monomers and the water bridges involved in ALys124. The unbinding process prediction showed that the PD-L1 dimerization kept stable upon the dissociation of ligands. It's indicated that the formation and stability of the small-molecule inducing PD-L1 dimerization was the key factor for the inhibitory activities of these ligands. The contact analysis, R-group based quantitative structure-activity relationship (QSAR) analysis and molecular docking further suggested that each attachment point on the core scaffold of ligands had a specific preference for pharmacophore elements when improving the inhibitory activities by structural modifications. Taken together, the results in this study could guide the structural optimization and the further discovery of novel small-molecule inhibitors targeting PD-L1.

Using small molecules to inhibit the PD-1/PD-L1 pathway is an important approach in cancer immunotherapy. Natural compounds such as capsaicin, zucapsaicin, 6-gingerol and curcumin have been proposed to have anticancer immunologic functions by downregulating the PD-L1 expression. PD-L1 dimerization promoted by small molecules was recently reported to be a potential mechanism to inhibit the PD-1/PD-L1 pathway. To clarify the molecular mechanism of such compounds on PD-L1 dimerization, molecular docking and molecular dynamics simulations were performed. The results evidenced that these compounds could inhibit PD-1/PD-L1 interactions by directly targeting PD-L1 dimerization. Binding free energy calculations showed that capsaicin, zucapsaicin, 6-gingerol and curcumin have strong binding ability with the PD-L1 dimer, where the affinities of them follow the trend of zucapsaicin > capsaicin > 6-gingerol ≈ curcumin. Analysis by residue energy decomposition, contact numbers and nonbonded interactions revealed that these compounds have a tight interaction with the C-sheet, F-sheet and G-sheet fragments of the PD-L1 dimer, which were also involved in the interactions with PD-1. Moreover, non-polar interactions between these compounds and the key residues Ile54, Tyr56, Met115 and Ala121 play a key role in stabilizing the protein–ligand complexes in solution, in which the 4′-hydroxy-3′-methoxyphenyl group and the carbonyl group of zucapsaicin, capsaicin, 6-ginger and curcumin were significant for the complexation of small molecules with the PD-L1 dimer. The conformational variations of these complexes were further analyzed by free energy landscape (FEL) and principal component analysis (PCA) and showed that these small molecules could make the structure of dimers more stable. This work provides a mechanism insight for food-derived small molecules blocking the PD-1/PD-L1 pathway via directly targeting the PD-L1 dimerization and offers theoretical guidance to discover more effective small molecular drugs in cancer immunotherapy.

Targeting PD-L1 and PD-1 interactions is a relatively new therapeutic strategy used to treat cancer. Inhibitors of PD-1/PD-L1 include peptides, small molecule chemical compounds, and antibodies. Several approved antibodies targeting PD-1 or PD-L1 have been patented with good curative effect in various cancer types in clinical practices. While the current antibody therapy is facing development bottleneck, some companies have tried to develop PD-L1 companion tests to select patients with better diagnosis potential. Meanwhile, many companies have recently synthesized small molecule inhibitors of PD-1/PD-L1 interactions and focused on searching for novel biomarker to predict the efficacy of anti-PD-1/PD-L1 drugs. This review summarized clinical studies and patent applications related to PD-1/PD-L1 targeted therapy and also discussed progress in inhibitors of PD-1/PD-L1.

Research into PD-L1 is critical in the development of small-molecule anti-cancer drugs. The current chemical compounds that bind to PD-1/PD-L1 exhibit lower efficacy than clinically relevant monoclonal antibodies, necessitating the need for new inhibitors. The aim of this study was to identify and characterise small-molecule inhibitors of PD-1/PD-L1 interaction. In this study, 1,900 compounds were screened against the PDL-1 target to identify binders using the ICM program. Virtual characterization by SwissADME of chemical scaffolds exhibiting high binding affinity to PD-L1 was performed. This was followed by the evaluation of the compounds for their PD-L1/PD-1 inhibitory activity in an in vitro ELISA assay, compared to the control. Analysis of the inhibition of the PD-L1 and PD-1 interaction revealed significant inhibition of the interaction with four compounds (Compound 3; X86577), (Compound 4; X02079), (Compound 6; X53550), and (Compound 9; X14474) compared to the anti-PD-1 neutralizing antibody. The findings present optimised small-molecule inhibitors targeting the PD-1/PD-L1 pathway, which could serve as effective immune checkpoint inhibitors. This work provides valuable insight into therapeutic solutions in addressing unmet medical needs in the oncology field.

BackgroundPD-1/PD-L1 antibody-based therapies have demonstrated tremendous success in the treatment of a variety of cancers. However, these antibody drugs are associated with several disadvantages, such as weak tumor penetration, immune-related...

69O - A small molecule human PD-1/PD-L1 inhibitor promotes T cell immune activation and reduces tumor growth in a preclinical model

Clinical Significance of PD-1 and PD-L1 Expression and Ongoing Interaction in the Tumor Microenvironment in Diffuse Large B Cell Lymphoma (DLBCL) Treated with R-CHOP

Evidence suggests that programmed death receptor-1/programmed death ligand-1 (PD-1/PD-L1) targeted inhibitors act as an immune checkpoint blockade, indicating that these compounds may be useful in cancer immunotherapy by inhibiting the immune response between T-cells and tumors. Previous studies have shown that ginsenosides can regulate the expression of PD-1 and PD-L1 in target diseases; however, it remains unknown whether ginsenosides act as a blockade of PD-1/PD-L1 interactions. In this study, we used competitive ELISA to investigate 12 ginsenosides for their ability to block PD-1/PD-L1 interactions. In addition, we performed a protein–ligand docking simulation and examined the hydrophobic interactions and hydrogen bonds formed at the interfaces between the ginsenosides and PD-L1/PD-1. Eight out of the 12 ginsenosides studied showed inhibition of PD-1/PD-L1 interactions at 35% at the maximum concentration (1 μM). Among them, Rg3 and Compound K (C-K) demonstrated the highest inhibitory effects. Rg3 and C-K were further identified for their interaction efficacy with PD-1/PD-L1, which supported our results demonstrating the blocking activity of these compounds against PD-1/PD-L1 binding interactions. Collectively, our findings suggest that some ginsenosides, including Rg3 and C-K, inhibit PD-1/PD-L1 binding interactions. Therefore, these compounds may prove useful as part of an overall immuno-oncological strategy.

In the field of cancer immunotherapy, the development of small-molecule inhibitors targeting the PD-1/PD-L1 signaling pathway has emerged as a pivotal research direction to overcome the clinical limitations of current antibody-based therapeutics. Based on the lead compound BMS-202, this study systematically elucidated the dynamic binding mechanisms of three novel inhibitors (BMS-202, LP23, A56) with the PD-L1 dimer through molecular dynamics simulations and multifaceted analysis. Results demonstrated that A56 exhibits superior binding stability and the strongest binding affinity among the three compounds, primarily due to its strong van der Waals (vdW) and electrostatic interactions with Chain B, whereas LP23 predominantly engages with Chain A via favorable electrostatic contributions. The alanine scanning method identified several key hotspot residues (Y56(B), M115(A/B), Y123(A), K124(A), etc.) that were crucial for inhibitor binding. Notably, the A56/PD-L1 system involved the most hotspot residues, which played an important role in enhancing binding affinity. Further analyses through dynamic cross-correlation matrix (DCCM) and principal component analysis (PCA) confirmed the highest structural rigidity and substantial correlated motions in the A56/PD-L1 complex, suggesting that A56 may achieve blockade of immune checkpoint signaling by stabilizing the closed conformation of the PD-L1 dimer and thereby dynamically occluding the PD-1/PD-L1 interaction interface. These findings elucidated the different binding mechanisms of novel small-molecule inhibitors to PD-L1 from both energy and conformational perspectives, providing a potential structural basis for the optimized design of immune checkpoint inhibitors.

We hypothesized that photodynamic therapy (PDT) with Chlorin e6 (Ce6) enhances antitumor abscopal effects via inhibition of the programmed cell death-1/programmed death-ligand 1 (PD-1/PD-L1) immune checkpoint. By using syngeneic melanoma and pancreatic tumor mouse models, we studied the Ce6-PDT-induced immune responses in local and distant tumor microenvironments. In addition, the Ce6-PDT's target in the PD-1/PD-L1 interaction was analyzed in MC38-hPD-L1 colon cancer and PD-1 expressing Jurkat T cell coculture. The tumors in the irradiated and non-irradiated sites in the abscopal effective (Abseff) group of both mouse models were regressed, proving the abscopal effect. The immunogenic effect in the Abseff group was associated with an expansion of T cell and other immune cells infiltration without changes in the CD39+ population in either the right or left tumors compared to control group. Furthermore, the abscopal ineffective (Absineff) group demonstrated lesser increase of T cells, decreased immune cell infiltration, and increased CD39-expressing Treg cells without suppression of tumor growth. In the coculture with PD-1-expressing Jurkat T cell, Ce6-PDT efficiently suppressed the PD-1/PD-L1 interactions by increasing the proliferation and cytotoxic activity of CD8+ T cells while decreasing CD39-expressing Treg cells in a dose-dependent manner. Likewise, the inhibition of PD-1/PD-L1 interactions was also correlated with the increased production of IL-2 and Granzyme B. Our findings imply that Ce6-PDT is a promising immunotherapy with the potential to improve the abscopal effect.

Genetic mutations accumulated overtime could generate many growth and survival advantages for cancer cells, but these mutations also mark cancer cells as targets to be eliminated by the immune system. To evade immune surveillance, cancer cells adopted different intrinsic molecules to suppress immune response. PD-L1 is frequently overexpressed in many cancer cells, and its engagement with PD-1 on T cells diminishes the extent of cytotoxicity from the immune system. To resume immunity for fighting cancer, several therapeutic antibodies disrupting the PD-1/PD-L1 interaction have been introduced in clinical practice. However, their immunogenicity, low tissue penetrance, and high production costs rendered these antibodies beneficial to only a limited number of patients. PD-L1 dimer formation shields the interaction interface for PD-1 binding; hence, screening for small molecule compounds stabilizing the PD-L1 dimer may make immune therapy more effective and widely affordable. In the current study, 111 candidates were selected from over 180,000 natural compound structures through virtual screening, contact fingerprint analysis, and pharmacological property prediction. Twenty-two representative candidates were further evaluated in vitro. Two compounds were found capable of inhibiting the PD-1/PD-L1 interaction and promoting PD-L1 dimer formation. Further structure optimization and clinical development of these lead inhibitors will eventually lead to more effective and affordable immunotherapeutic drugs for cancer patients.

Targeting the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) axis with monoclonal antibodies (mAbs) represents a crucial breakthrough in anticancer therapy, but mAbs are limited by their poor oral bioavailability, adverse events in multiple organ systems, and primary, adaptive, and acquired resistance, amongst other issues. More recently, the advent of small molecule inhibitors that target the PD-1/PD-L1 axis have shown promising cellular inhibitory activity and the potential to counteract the disadvantages of mAbs. In this study, structure-based virtual screening identified small molecule inhibitors that effectively inhibited the PD-1/PD-L1 interaction. Six of those small molecule inhibitors were applied to cell-based experiments targeting PD-1: CH-1, CH-2, CH-3, CH-4, CH-5, and CH-6. Of all 6, CH-4 displayed the lowest cytotoxicity and strongest inhibitory activity towards the PD-1/PD-L1 interaction. The experiments revealed that CH-4 inhibited the interaction of soluble form PD-L1 (sPD-L1) with PD-1 surface protein expressed by KG-1 cells. Investigations into CH-4 analogs revealed that CH-4.7 effectively blocked the PD-1/sPD-L1 interaction, but sustained the secretion of interleukin-2 and interferon-γ by Jurkat cells. Our experiments revealed a novel small molecule inhibitor that blocks the interaction of PD-1/sPD-L1 and potentially offers an alternative PD-1 target for immune checkpoint therapy.

Introduction: FDA-approved antibody-based therapies targeting the Programmed cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) immune checkpoint axis have gained considerable attention and success in cancer immunotherapy recently. As a next-generation therapy, small-molecule PD-1/PD-L1 checkpoint inhibitors may provide the potential for increased tumor penetration, shorter half-life (to better manage immune related adverse events), and lower cost of goods. We embarked on an effort to identify and develop small molecules capable of targeting the immune checkpoint molecules PD-1/PD-L1, with an aim to improve anticancer immune responses in vivo. Methods: Co-crystallized human PD-1/PD-L1 provided structural information from which we developed a number of small-molecule checkpoint inhibitors. Active compounds were first profiled by an ELISA assay measuring inhibition of the PD-1/PD-L1 interaction, followed by functional cell-based reporter and mixed lymphocyte reaction (MLR) assays. PD-1/PD-L1 inhibitory compounds thus identified were further selected for in vivo model testing. Since our human-specific PD-1/PD-L1 inhibitors did not cross-react with murine PD-1/PD-L1, we co-implanted A375 human melanoma cells along with human peripheral blood mononuclear cells (PBMCs) into immunodeficient NOD/SCID mice to test their efficacy in vivo. Results: The optimized human PD-1/PD-L1 inhibitors exhibited marked activities in both the cell-based reporter and MLR assays. Moreover, lead compound CCX4503 reduced tumor growth in vivo to a similar extent as the positive control anti-human PD-L1 antibody. Antitumor activity was completely dependent on the presence of human PBMCs. The tumor microenvironment analysis by flow cytometry indicated that the antitumor activity of CCX4503 was accompanied by a significantly higher CD8+ T-Cell/CD4+ T-cell ratio. An X-ray structure of CCX4503 co-crystallized with PD-L1 revealed several vital interactions within the PD-1-binding-region of PD-L1, providing information about the structural basis by which the compound disrupts the PD-1/PD-L1 immune checkpoint interaction. Summary: We have identified and advanced unique small-molecule inhibitors of human PD-1/PD-L1 by rational design. Molecules resulting from these efforts, such as CCX4503, exhibited marked inhibition of the PD-1/PD-L1 interaction and signaling in vitro, and also clear antitumor effects in an animal model system in vivo. Citation Format: Marta Vilalta, Sreenivas Punna, Shijie “Chris” Li, Viengkham Malathong, Christopher Lange, Darren McMurtrie, Ju Yang, Howard Roth, Jeffrey McMahon, James J. Campbell, Linda S. Ertl, Ryan Ong, Yu Wang, Niky Zhao, Vicky Chhina, Alice Kumamoto, Simon Yau, Tong Dang, Penglie Zhang, Thomas J. Schall, Rajinder Singh. Tumor reduction by a small molecule human PD-1/PD-L1 inhibitor in a melanoma/PBMC co-implantation model [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B26.