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 at Substrate. This 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.

About Substrate 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.

The role You will own the chemistry strategy at Substrate. If 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.

What you will do in your first twelve months FIST 90 DAYS: 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.

MONTHS 4 TO 8 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 model-side work. Draft the strategy document iteratively. If trending toward greenlight, begin sketching the day-1 chemistry assay portfolio, the make/buy/precursor architecture, and the workcell shape that would carry them.

MONTHS 9 TO 12 Close the strategy. Present a clear recommendation to the co-founders: build a standalone chemistry vertical, hold the bet and fold chemistry into the existing verticals, or some variant in between. If the recommendation is greenlight: transition into Chemistry Lead build-out work, or into first-hire-under-Head-of-Chemistry mode, depending on which path the co-founders take. If the recommendation is hold: transition into chemistry support across the protein science and functional genomics verticals.

Who you are You are a chemist who is excited about an open scoping mandate rather than a defined assay portfolio. You enjoy research-mode work as much as hands-on bench work. You write good assessments and can hold a value‑proposition argument together while you go gather the evidence to test it. You have deep chemistry training and a working sense of the chemistry‑automation industry: what existing platforms can do, where their gaps are, and where customer quality requirements sit above what current instrumentation delivers. You can have a credible conversation with a pharma R&D chemist about what they actually use, or with a foundation‑model researcher about the chemical‑space coverage their model needs. You are comfortable working largely autonomously, with Alexey as your weekly thought partner and otherwise self‑directed. You are comfortable with the three‑fork future of this role and would rather know all three paths are real than have one of them sold to you.

MUST HAVE PhD in synthetic chemistry, medicinal chemistry, or a closely adjacent discipline. A couple of years of post‑PhD industrial experience (pharma R&D, biotech, or a chemistry‑flavoured CRO) where small molecule therapeutic candidate generation and characterisation were part of the day job. Working familiarity with the small molecule therapeutic assay landscape: binding, biophysical, ADMET, cell‑based characterisation, or analogous readouts. Working knowledge of automated, flow, and high‑throughput chemistry, and where the existing chemistry‑automation industry can and cannot reach today.

NICE TO HAVE Direct experience working with or alongside customers (pharma partners, foundation model labs, or AI‑native biotech) on assay or workflow design. Published work on automated, flow, or high‑throughput chemistry, or on closed‑loop generative chemistry workflows. Background near AI / ML, computational chemistry, or scientific computing. Experience working at the boundary between chemistry and other scientific disciplines (biology, screening, ADMET).

Why this is unusual Most senior chemistry roles at venture‑backed companies sit either inside an established platform that has already committed to chemistry, or inside a pharma R&D group running an internal chemistry pipeline. This is neither. You will be the person who decides whether Substrate commits to chemistry as a standalone vertical, by doing the work to figure out what shape that vertical should take and whether the case for it holds. Some chemists find that openness energising: the chance to scope a strategic bet, shape it from the ground up, and either lead the build‑out or hand it off to a more senior Head of Chemistry. If the standalone bet does not greenlight, chemistry expertise is still needed across our other verticals, so the work continues, just inside a different scope. Worth knowing in advance whether this kind of openness fits how you want to work.

Compensation and equity We pay competitively against the London market for PhD‑level chemists at venture‑backed companies, calibrated to seniority and to the specific scope of this role. We will discuss numbers with serious candidates after first conversations. Options on the standard four‑year vest with a one‑year cliff. The specific quantum reflects the scoping nature of the hire and will be discussed with serious candidates.

How we work Working pattern is hybrid with an in‑person bias dictated by the team. You will be at our King’s Cross site most days, particularly during the research‑mode phase where the work benefits from being close to Alexey and the rest of the founding team. If and when the chemistry vertical greenlights and bench work begins, the cadence shifts to lab‑based. 30 days annual leave. A learning budget you can use for conferences, courses, books, and time. The founding team operates on a weekly cadence with a Monday planning meeting and a Friday close, and a quarterly offsite. We are direct with each other, we write things down, and we expect to be challenged.

The team you will join You will report to Alexey Morgunov, our science and AI focused co‑founder. Alexey is your weekly thought partner on the strategy and your direction‑setter through the scoping phase. You will work alongside Mostafa on customer conversations, with foundation model labs primarily and with pharma R&D contacts secondarily, and with the Heads of Protein Science and Functional Genomics on a peer‑to‑peer basis. You are the first and currently only chemistry hire. Substrate is currently three co‑founders growing to roughly 32 people by the end of Q1 2027. Substrate is an equal opportunity employer. We make hiring decisions on merit, scope‑fit, and the strength of the working relationship we expect to build with each hire. Applications welcome from candidates of any background.