YDS Pharmatech's New Generative Diffusion Model Significantly Improves Structure-Based PROTAC Optimization and Ternary Interaction Analysis; Presentation at Drug Discovery Chemistry 2023 Conference

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Apr 07, 2023, 21:00 ET

ALBANY, N.Y., April 7, 2023 /PRNewswire/ -- A groundbreaking study by a team of scientists at YDS Pharmatech, Inc. has introduced an innovative Generative Diffusion Model (GDM) for sampling ensembles of degrader-induced ternary interactions, enabling a more effective approach to structure-based optimization of Proteolysis Targeting Chimeras (PROTACs). The new model provides an efficient method for modeling ternary complexes and enhances the understanding of ligand-induced protein-protein interactions.

Ternary complex interactions sampled by AI-augmented enhanced sampling molecular dynamics

Thermodynamics of PROTACs induced ternary complex interactions

YDS Pharmatech will present their findings at the upcoming Drug Discovery Chemistry 2023 conference, showcasing the potential of the GDM approach to significantly enhance PROTAC optimization and ternary interaction analysis.

Traditionally, structure-based optimization of PROTACs has been a challenging task due to the difficulty of accurately modeling ternary structures. Conventional computational methods, such as RosettaDock, predict protein-protein complexes and then attempt to fit molecules into the interface. However, these methods are often limited in their ability to fully capture the dynamic nature of ternary interactions.

Xing Che, CEO of YDS Pharmatech, shared his thoughts on the breakthrough: "Our research team's adoption of a generative diffusion model for sampling conformation ensembles and efficiently modeling ternary complexes has led to remarkable performance and new insights into the underlying mechanisms of PROTAC function. As one of the earliest adopters of using generative models for ternary thermodynamics interactions, I am amazed by the precision and insights from such modeling when our team presented the results."

"YDS Pharmatech is a company with impressive expertise in simulation and AI technology. We have had the pleasure of collaborating with YDS on several ternary complex modeling projects, and the results have been consistently promising. We are confident that our fruitful association with them will continue to bring valuable insights and positively impact the progress of our research." Commented by Kota Murasaki, Computational chemist of Mitsubishi Tanabe Pharma Corporation.

About YDS Pharmatech, Inc.:

YDS Pharmatech, Inc. is a drug discovery company developing computational platforms for multispecific drugs. The company uses AI-accelerated enhanced sampling molecular dynamics simulations to study ternary complex interactions, thermodynamics, and kinetics. Endeavoring to contribute to induced proximity studies and making degrader discovery transition from serendipitous to rational design. YDS Pharmatech focuses on PROTACs and molecular glue protein degraders at its current stage. Their interdisciplinary team of scientists collaborates with researchers worldwide to pioneer innovative treatments for various diseases.

SOURCE YDS Pharmatech, Inc.