Merck Taps Protillion for AI Protein Design

Editor’s Take: Merck is the latest global pharmaceutical company to deepen its investment in AI-enabled drug discovery.

Merck, known as MSD outside the United States and Canada, has signed a multi-target discovery collaboration and license agreement with Protillion Biosciences Inc., an expert in lab-in-the-loop AI drug design. The agreement combines Protillion’s proprietary platform with Merck’s global expertise in the discovery of novel therapeutic candidates.

Protillion’s proprietary Prot-MaP technology is a megascale data generation platform purpose-built to deliver massive, just-in-time training sets to protein design AI (Megascale Data + AI). Protillion claims that this approach enables the quantitative analysis of protein libraries with “unprecedented throughput,” characterizing millions of variants per run and avoiding the common pitfalls of model overfitting. This enables the identification of optimized biologics with sophisticated therapeutic profiles—such as pH-dependent sweeping and multi-target specificity—that are difficult to achieve with traditional methods.

Under the terms of the agreement, Protillion will receive an undisclosed upfront payment and is eligible to receive research, development, and commercial milestone payments of up to $510 million for the successful development of multiple therapies.

“Merck is a global leader in biopharmaceutical innovation, making them an ideal partner to deploy our technology,” said Curtis Layton, Ph.D., CEO and Co-founder of Protillion Biosciences. “This relationship underscores the power of our platform to solve complex protein engineering challenges. We are thrilled to work alongside the Merck team to deliver better medicines to patients faster.”

“Powerful emerging technologies offer the potential to transform the speed and precision with which we characterize protein landscapes and identify novel therapeutic candidates,” said Juan Alvarez Ph.D., Vice President Discovery Biologics, Merck Research Laboratories. “Protillion’s platform offers a compelling opportunity and we look forward to working with the team to advance these programs.”

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