Chemistry Principal Scientist

The opportunity

Substrate is building a network of fully autonomous wet labs, cloud-based data production facilities for AI biology, integrated with foundation models to become the critical infrastructure layer for AI-driven biological discovery. Our first node opens in King’s Cross, London, with several integrated workcells and two scientific verticals, protein science and functional genomics, online by mid-2027. Our customers range from foundation model labs to global pharma.

We are hiring a Chemistry Principal Scientist to develop the strategy for chemistry s is a deliberately exploratory hire. Your job is to figure out what shape a chemistry vertical should take, whether the case for it holds, and what the day-1 architecture should look like if it does. Depending on what you find, the role evolves: you may grow into the Chemistry Lead position, a Head of Chemistry may be recruited above you, or your chemistry expertise folds into the protein science and functional genomics verticals where it is needed regardless.

All three paths are real.

Substrate is spinning out of Automata, the UK lab automation company that has built the workcell platform our labs run on. Our four co-founders are Mostafa ElSayed (CEO and founder of Automata), Oli Hoy (formerly VP Customer Experience at Automata), Alexey Morgunov (AI Scientist co-founder, leading the intelligence software product), and a Founding Biology Lead joining shortly. We are aiming to have ramped up to 32 people by the end of Q1 2027.

We are funded in parallel by a combination of venture funding and government grants. We are not a cloud lab and we are not a CRO. We are an autonomous lab platform with closed-loop integration available as one operating mode for foundation model partners.

You will own the chemistry strategy  we build the vertical, it will mirror our protein science vertical but for small molecule therapeutic candidates: making the molecules through some combination of on-site synthesis, pre-sourced precursors with on-site coupling, and external procurement, and testing them through a portfolio of characterisation assays designed for closed-loop work with generative AI. The use case we are most interested in is a model asking for a large set of candidate molecules and Substrate making and testing what is possible quickly, in a tighter cycle than current CROs can deliver.

Your job is to develop the strategy for this space: the right architecture for the make/buy/precursor decision tree given the molecule classes our customers most need, the day-1 assay portfolio that sits on top of these candidates, where the gaps are in what existing automated chemistry platforms can do, and where the customer demand signal sits between foundation model labs and pharma R&D.

You will spend significant time with Alexey as a weekly thought partner; otherwise the work is autonomous and self-directed. You will write up the strategy iteratively and present a clear recommendation to the co-founders by roughly month nine to twelve. If the recommendation is to build, you may grow into the Chemistry Lead position, or a Head of Chemistry may be recruited above you.

If the recommendation is to hold, the role evolves into chemistry support across the protein science and functional genomics verticals (conjugation work, small molecule perturbations, related supply-chain decisions) rather than ending.

You will write up the strategy iteratively and present a clear recommendation to the co-founders by roughly month nine to twelve. If the recommendation is to build, you may grow into the Chemistry Lead position, or a Head of Chemistry may be recruited above you. If the recommendation is to hold, the role evolves into chemistry support across the protein science and functional genomics verticals rather than ending.

• Land in the team. Set up workspace at our King’s Cross site and start the strategy scan in two directions: the foundation-model landscape for generative chemistry, and the chemistry-automation industry.

• Map the chemical-space coverage problems the model builders are prioritising. Map the gaps in what existing automated chemistry platforms can do today, especially where customer quality requirements sit above the line.

• Begin customer conversations alongside Mostafa with foundation model labs and pharma R&D contacts. Learn what they find painful when working with CROs today, and what is already commodity for them.

• Sharpen the strategy. For each candidate molecule class and assay readout, assess what Substrate could realistically operate at quality, what mix of on-site synthesis and external procurement makes sense, and what the customer demand signal looks like.

• Continue tracking the foundation-model landscape as it evolves. Which generative-chemistry directions are converging on something Substrate’s autonomous chemistry could become the execution layer for, and which are still purely…