Lab Rats series: A Bengaluru startup’s bid to drug the undruggable

Mumbai: In the mid-2010s, a scientist and a software engineer met through their children, frequently running into each other outside birthday parties and school events. Conversations fixated on what was new in their professional worlds: drug discovery for Shridhar Narayanan, former head of research and development (R&D) at AstraZeneca’s Bengaluru lab, and machine learning for software engineer Venkatasubramanian Narayanan, known better as just Venkat.

These casual interactions eventually evolved into serious discussions on how technology and artificial intelligence (AI) could intersect with drug discovery, culminating in the establishment of an AI-driven drug discovery platform. The goal was to leverage AI to accelerate discovery timelines while targeting hard-to-treat diseases with significant unmet medical needs.

Founded in 2019, Peptris Technologies was incubated at the sprawling Centre for Cellular and Molecular Platforms (C-CAMP) campus in Bengaluru. Its proprietary AI platform accelerates the discovery of potential molecules ready for wet-lab testing and expands the scope of diseases and drug targets for which candidate molecules can be identified.

However, the startup is not alone in this space. As biotech firms and major pharmaceutical companies increasingly turn to AI to compress early-stage timelines, Peptris faces the challenge of carving out a distinct niche to remain competitive and agile both in India and globally. It is actively working to establish that edge, backed by recent capital raised through a Series A funding round as well as a grant from the government’s flagship Research, Development and Innovation (RDI) Fund.

AI models are increasingly being used to design molecules tailored for complex proteins previously deemed “undruggable”—targets where conventional molecules were historically unable to latch on.

Peptris uses the platform to generate novel molecules, as well as find new targets or disease indications for previously approved drugs.

Peptris has already out-licensed one of its repurposed drug candidates, PEPR124 (RT001), to Revio Therapeutics for Duchenne muscular dystrophy (DMD), a rare, fatal neuromuscular disorder with few treatment options. It has a high unmet need, affecting roughly 400,000 people in India.

Peptris’s molecule, originally used to treat diabetes, received orphan drug designation from the US Food and Drug Administration (USFDA) to accelerate its clinical pathway for the molecule. An orphan drug designation is a special status granted by the USFDA for drugs intended to treat rare diseases, and offers various incentives like market exclusivity, fee waivers and regulatory assistance.

The focus, the founders said, is to continue finding molecules for diseases with high unmet needs. There are an estimated 7,000 rare diseases today, of which 95% have no cure yet. “That’s the scale of the problem,” said Venkat, the chief executive officer (CEO). Peptris’s pre-clinical pipeline primarily includes drugs focused on rare diseases.

The pipeline

Peptris has a vast pipeline of pre-clinical assets, working across oncology, rare diseases, inflammation and other therapy areas. Earlier this month, the firm secured ₹86 crore under the government’s RDI Fund and plans to advance four of its assets through preclinical development.

“The advantage with using a technology like the one that we have is that it is agnostic to the disease area, and to the therapeutic target,” said Shridhar, chief scientific officer at Peptris.

This approach helps Peptris mitigate a major risk inherent to traditional biotech startups—relying heavily on the development of a single lead asset, which typically carries a binary success-or-failure outcome.

Additionally, the startup’s algorithm is designed to identify “off-targets” for a given molecule—evaluating how it might bind to proteins beyond its primary intended target.

Where does it stand?

AI-led drug discovery is currently the defining trend in biopharma, and for good reason. Google DeepMind’s AlphaFold system marked a milestone breakthrough by predicting 3D protein structures, earning its developers the 2024 Nobel Prize in Chemistry.

Building on this foundation, AI-powered biotechs like Insilico Medicine have advanced toward clinical validation, deploying generative AI to identify targets and design molecules that are now in human trials.

Several other global AI-driven drug discovery startups operate capex-heavy models to construct automated high-throughput labs and run extensive internal clinical pipelines.

Peptris operates within the generative-chemistry layer, deploying AI to generate and optimize small molecules while predicting their drug-like properties across a preclinical pipeline. It benchmarks its performance against global open-source models like the highly regarded Boltz 2.

“We know how well we are performing… we are doing pretty well on some of the targets, not doing well with some of them, so we know that it's a work in progress,” said Venkat.

Beyond AI

Despite the hype, a degree of pragmatism remains essential in this landscape, according to Venkat. “Drug discovery is not about just the first prediction AI comes with,” he said. “You really need to go through the rigor of it. Try it out at first at the biochemical level, at a cellular level, then at an animal level… AI can accelerate each of these (discovery and development) phases but AI is not solving the problem. It is helping real biologists, real clinicians and chemists solve the problem.”

Ultimately, the company’s model combines technology, scientific expertise and India’s cost advantage.

Indian biotechs must identify distinct niches within a globally competitive market to differentiate themselves, said Dr Taslimarif Saiyed, CEO and director of C-CAMP. “When there is a huge rush for cancer, for autoimmune diseases, etc., how does one look at it from a new approach and stand out? That is important,” he said. For Peptris, “it is a combination of convergence of deep expertise, plus availing highly accessible early-stage capabilities, and a cost advantage where you can do more in less money.”

With fresh capital secured, Peptris aims to transition into a full-fledged discovery and development firm, bringing more development in-house. Beyond the government’s RDI grant, it raised ₹70 crore in a Series A funding round led by IAN Alpha Fund and Speciale Invest in February.

“About six months ago we would still be calling ourselves an AI-powered drug discovery company,” said Shridhar. “Now, there is a definite path forward to take a little more risk, be a little more aspiring in terms of where we want to reach before we out-license our molecules.”

This is the fifth in a six-part Mint series on biotech startups.