The process of identifying promising small molecule drug candidates that target cancer checkpoints may become faster and smarter through virtual screening, according to Weill Cornell Medicine researchers.

Checkpoint inhibitors are a type of immunotherapy that treats cancer by releasing the brakes on immune cells, so they are unleashed to attack cancer cells. Currently, all approved checkpoint inhibitors are large, lab-made proteins called monoclonal antibodies which must be infused into the bloodstream. They block the binding of checkpoint proteins with their partner proteins, preventing the “off” signal that stops immune T cells from being activated. 

“Our research represents a remarkable advancement in the field of cancer immunotherapy, which may lead to a promising alternative to monoclonal antibody-based treatments,” said senior author Moustafa Gabr, assistant professor of chemistry in radiology.

Credit: Gabr Lab/Provided

The findings published, Oct. 16 in Science Advances, demonstrate a way to virtually screen millions of compounds to find small molecules with the potential to bind checkpoints allowing the immune system to mount an attack against cancer. Small molecules have an advantage because they are generally orally bioavailable for easier administration, tailored dosing and improved patient compliance. They can also penetrate tumors more effectively due to their smaller size. 

The first author on the paper is Somaya Abdel-Rahman, an assistant professor of pharmacy in the department of medicinal chemistry, Mansoura University, Egypt.

The difficulty in targeting immune checkpoint proteins is their flat and dynamic surfaces, which don’t bind small molecules easily. To address this issue, Gabr and Abdel-Rahman looked to the co-crystal structures of immune checkpoints bound to monoclonal antibodies.

The researchers used a computational tool that identifies key interacting sites within the protein-protein interfaces of monoclonal antibody-bound checkpoint proteins. This helped them generate “pharmacophore” maps, three-dimensional models that show the essential features of the binding interactions. They then calculated properties such as how tightly the molecules bind together and “druggability” scores, which are essential for the rational design of small-molecule inhibitors. 

This analysis guided the virtual screening of a database including millions of commercially available small molecules. The potential hits identified mimicked the binding interactions of monoclonal antibodies with their target checkpoints. 

The most promising compounds were further tested to confirm binding affinity – how tightly the molecule interacted with the checkpoint protein – and specificity – the ability of the compound to bind only the intended target. They also tested the compounds in cells to assess the functional impact of the small molecules on immune checkpoint activity.

This study identified a molecule called MG-T-19, which strongly inhibited TIM-3, a checkpoint receptor expressed by a wide variety of immune cells. TIM-3 is an inhibitory checkpoint that, when blocked, can reinvigorate T cell responses against tumors.

Another compound, MG-V-53, was identified as a VISTA inhibitor with in vivo antitumor activity. VISTA is another inhibitory checkpoint implicated in tumor immune evasion.

“The small molecules identified in this study not only exhibit strong binding affinities but also show promising activity in mouse models, including reducing the volume of tumors,” Gabr said. This suggests their potential for therapeutic development.” 

Future studies will focus on optimizing the top-hit compounds for clinical use, exploring their synergistic effects in combination therapies and expanding this unique screening approach to additional immune targets.

“This approach has the potential to expand the repertoire of available cancer therapies, improving patient outcomes and opening new avenues for research and development,” Gabr said.

Karen Hopkin is a freelance writer for Weill Cornell Medicine.