Pepper Bio, backed by NFX, breaks out of stealth with tools to focus on complex diseases

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There is an obvious problem when it comes to drug discovery: According to the study you cite, creating an approved drug costs $ 985 million To $ 2.6 billion. And R&D returns rebounded to just about 2.5% in 2020, from a low of 1.6% in 2019. Not to mention the fact that drugs that fail in clinical trials don’t actually help people who need new treatments.

With a problem like this, it’s no surprise that we’ve seen countless startups enter the drug development arena, each looking to carve out their own niche. Perhaps this is AI-powered drug discovery, advanced proteomics (the study of proteins and their interactions) or, for a new business, layers upon layers of biological data.

On Thursday, Pepper Bio, a Boston-based startup company, came out of stealth. Pepper Bio has built a “compute platform,” in the words of co-founder and scientific director Samantha Dale Strasser, who the company says can aid in drug discovery.

Pepper Bio worked with several layers of biological data. This includes genetic data, proteomics, transcriptomics (the study of RNAs, coding or not, that exist in a cell) and phosphoproteomics – that is, when a phosphate group is added to a protein and thus changes its function.

To break this down further: Think of the genetic part as a roadmap for the body’s proteins. Think of proteomics as the study of how these routes (proteins) interact and cross. Phosphoproteomics is the study of protein phosphorylation – essentially, a process by which the body adds a chemical label to proteins and changes their function. Think of them as cars on the road. Transcriptomics is just another layer of traffic data that changes in real time.

Overall, Pepper Bio describes itself as a “Waze for Drug Discovery” because its developing computing platform is able to extract these layers of information from experimental data.

“The idea behind global causal and functional data and analysis is that we are much better equipped to manage very complex diseases,” says Jon Hu, CEO and co-founder of Pepper Bio.

Pepper Bio representatives would not disclose the full amount of funding the company has raised so far. The company has already raised a pre-seed round and is currently raising a seed round. The company is backed by NFX, also an investor in Mammoth Biosciences.

To date, the company has four employees.

The founders of Pepper Bio fashioned Pepper Bio around their own brushes with the disease. Hu struggled with chronic migraines and managed to control the disease. However, when his grandmother was diagnosed with Alzheimer’s disease (a disease with a highly controversial single treatment option), he found himself lost.

Strasser had the same feeling when his father was diagnosed with dementia. Doctors could monitor the progression of the disease, but not stop it.

“It was the first step – just feeling how your world comes to a stop when this happens,” Strasser says.

Pepper Bio’s answer to the drug discovery problem appears to be the accumulation (and analysis) of biological data. But the real added value of Pepper Bio, according to Strasser, is the addition of the transcriptomic and phosphoproteomic components.

“We provide information on modified proteins. This is what gives Pepper’s technology the ability to examine this data and have a functional understanding of what is going on in drug discovery, ”says Strasser.

So far, some general research papers suggest that this approach can be used to find therapeutic targets. One of the Strasser papers 2019 in Integrative biology specifically applied the phosphoproteomic analysis process to two mouse models of inflammatory bowel disease.

Specifically, the technique identified a kinase that was activated in mouse models. In a follow-up experiment, animals with colitis (an inflamed colon) were treated with an oral drug that appeared to block activity in the identified pathway. In essence, the article was a proof of concept that phosphoproteomics can identify relevant targets for preclinical studies.

Going forward, Pepper Bio has yet to demonstrate that it can use its approach to generate new potential drug targets. So far, the company has two partnerships, Hu said. One is with a clinical-stage “central nervous system enterprise” in which Pepper Bio helps profile a potential drug and shed light on how it actually works. Pepper Bio is currently writing a paper manuscript with this company.

The company also works alongside an oncology lab at Stanford led by Dean Flesher, director of translational and applied medicine at Stanford University School of Medicine. The company aims to create a solid tumor dataset, develop a clinical prediction algorithm and identify new therapeutic targets, according to Hu.

From a business perspective, the company is not intended to be simply a drug discovery platform that others can use. As Hu notes, they would like to retain the option of developing their own clinical pipeline of conditions – although Hu says it could take “three or four years” down the line.

For now, the company will measure its success in terms of being able to build its own databases (to include more information on proteins, transcriptomes or phosphorylation), and pursuing more partnerships with research institutes or drug manufacturers.

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