Pepper Bio: AI-Powered Tools for Complex Disease Research

The High Cost of Drug Development and Emerging Solutions

The process of bringing a new drug to market presents a significant financial challenge. Estimates suggest the cost of creating an approved drug ranges from $985 million to $2.6 billion, depending on the source.

Furthermore, returns on research and development (R&D) investments have only recently improved, reaching approximately 2.5% in 2020, a rise from 1.6% in 2019. Crucially, clinical trial failures do not translate into benefits for patients in need of novel treatments.

A Surge of Startups in Drug Discovery

Given these substantial hurdles, it’s unsurprising that numerous startups are entering the drug development arena, each seeking to establish a unique position. Many are focusing on areas like AI-based drug discovery or advanced proteomics – the comprehensive study of proteins and their interactions.

Others, like a recently launched company, are leveraging extensive layers of biological data to accelerate the process.

Introducing Pepper Bio: A Computational Platform for Drug Discovery

Pepper Bio, a seed-stage company headquartered in Boston, officially launched on Thursday after operating in stealth mode. The company is constructing a “computational platform,” as described by co-founder and chief scientific officer Samantha Dale Strasser, designed to facilitate advancements in drug discovery.

Pepper Bio’s approach centers on integrating multiple layers of biological data, including genetic information, proteomics, transcriptomics (the study of RNA molecules within cells), and phosphoproteomics.

Understanding the Layers of Biological Data

To clarify, genetic data can be viewed as a blueprint for the body’s proteins. Proteomics examines how these proteins interact. Phosphoproteomics investigates the modification of proteins through phosphorylation, a process that alters their function.

Think of phosphorylation as adding chemical tags to proteins, influencing their activity – akin to vehicles traveling on a road network. Transcriptomics provides real-time traffic data, reflecting dynamic changes within the system.

Pepper Bio characterizes its platform as a “Waze for drug discovery,” capable of extracting meaningful insights from these complex data layers.

Pepper Bio’s Vision and Funding

“Our strategy of incorporating comprehensive causal and functional data and analysis equips us to address highly complex diseases more effectively,” explains Jon Hu, CEO and co-founder of Pepper Bio.

While the company has not disclosed the total funding received to date, Pepper Bio has secured a pre-seed round and is currently raising a seed round. NFX, an investor in Mammoth Biosciences, is among the company’s backers.

Currently, Pepper Bio operates with a team of four employees.

Personal Experiences Fueling Innovation

The founders of Pepper Bio are personally motivated by their experiences with disease. Hu has successfully managed chronic migraines, but his grandmother’s diagnosis of Alzheimer’s – a condition with limited treatment options – left him feeling helpless.

Strasser shared a similar sentiment when her father was diagnosed with dementia, highlighting the challenges of tracking disease progression without the ability to halt it.

“It’s a profoundly disorienting experience when faced with such a situation,” Strasser states.

The Value of Integrated Data Analysis

Pepper Bio’s core strategy involves accumulating and analyzing biological data. However, Strasser emphasizes the significance of incorporating transcriptomics and phosphoproteomics.

“By including information on modified proteins, our technology gains a functional understanding of the processes occurring during drug discovery,” says Strasser.

Existing research supports this approach, with studies demonstrating its potential for identifying therapeutic targets. A 2019 paper authored by Strasser, published in Integrative Biology, applied phosphoproteomic analysis to mouse models of inflammatory bowel disease.

Proof of Concept: Phosphoproteomics in Action

The study identified a specific kinase activated across the mouse models. Subsequent treatment with an oral drug targeting this pathway showed promising results in animals with colitis (inflammation of the colon). This served as a proof of concept for using phosphoproteomics to pinpoint relevant targets for preclinical research.

Future Directions and Partnerships

Moving forward, Pepper Bio aims to validate its approach by identifying novel drug targets. The company has already established two partnerships.

One collaboration involves a clinical-stage central nervous system company, where Pepper Bio is assisting in profiling a potential drug and elucidating its mechanism of action. A manuscript detailing this work is currently in preparation.

Pepper Bio is also collaborating with an oncology lab at Stanford University, led by Dean Felsher. The goal is to create a comprehensive dataset on solid tumors, develop a clinical prediction algorithm, and identify new therapeutic targets.

Beyond a Platform: Potential for Pipeline Development

From a business standpoint, Pepper Bio does not intend to solely function as a drug discovery platform for others. Hu notes the company wishes to retain the option of developing its own clinical pipeline, potentially “three or four years” from now.

Currently, the company will gauge success by its ability to expand its databases – incorporating more data on proteins, transcriptomes, and phosphorylation – and by forging additional partnerships with research institutions and pharmaceutical companies.