Senior Computational Chemist

The role

Join Aqemia in a role where you will design the molecules that move our drug discovery programs forward, from hit identification through lead optimization and towards pre-clinical candidate nomination.

Working side by side with medicinal chemists, biologists, physicists and machine learning scientists, you’ll combine physics-based modeling, generative AI and medicinal chemistry insight to decide which molecules we make and why, across internal programs and pharma partnerships. This is not a role where you apply tools in a box: you’ll bring new methods into live projects, test them against experimental data, and help shape how our AI and platform teams build the next generation of design capabilities, including AI agents for molecular design and autonomous computational workflows. Within your first year, you’ll own key design decisions on your programs and become a go-to scientific voice in our drug discovery team.

Responsibilities

• Design, prioritize and optimize small molecules across multiple programs to drive compounds from hit identification through lead optimization to candidate nomination

• Own the design hypothesis: set clear, testable hypotheses, separate what we know from what we believe, and change course quickly when the evidence changes

• Bring the full computational toolkit to each design question, including structure- and ligand-based design, docking, molecular dynamics, free energy calculations, chemoinformatics and generative AI

• Integrate biochemical, biophysical, pharmacological and ADME-Tox data with predictions to spot trends, risks and opportunities, and turn them into clear recommendations on what to make next

• Pilot new technology in live projects: put AQEMIA’s generative and predictive models, AI agents and automated workflows to the test, benchmark them, and feed back what works to our platform and ML teams

• Partner daily with medicinal chemists, biologists, ML scientists, physicists and project managers on internal programs, pharma collaborations and early-stage pre-program work

• Communicate findings, recommendations and risks clearly and directly in project reviews and strategy discussions, flagging early when a result changes the plan

Qualifications

• PhD in computational chemistry, medicinal chemistry, chemical biology, biophysics or a related discipline, or a Master’s in a relevant field with equivalent depth of industry experience

• 3+ years of industry experience (pharma, biotech or CRO) in small molecule drug discovery, working in integrated project teams alongside medicinal chemists and biologists

• Hands-on contribution to programs across hit identification, hit-to-lead and lead optimization as a core design contributor, not only in a narrow specialist role

• Strong expertise in structure-based and ligand-based drug design, protein-ligand interactions and medicinal chemistry principles

• Practical experience with docking, molecular dynamics, free energy methods and chemoinformatics, using tools such as RDKit, OpenMM, AmberTools, GROMACS or equivalent

• Working proficiency in Python and Linux: comfortable running, reading and adapting scripts and computational workflows

• A direct, evidence-driven communicator who is clear about what you know, what you don’t, and what you would do next

Why Join Us ?

At AQEMIA, we work for a mission: joining us means having your own impact on changing the way drugs are discovered, and helping to shape the direction of our fast-growing company and team.

Expanding Drug Discovery Pipeline: Focused on critical therapeutic areas like Oncology, CNS, Immuno-inflammation... with in vivo proof of concept/patent stage programs. Collaborations with top Pharma, including a $140M Sanofi deal.

World-Class Interdisciplinary Team: work alongside exceptional talent at the intersection of technology and life sciences. Our teams combine deep expertise in AI, physics-based modeling, biology, and medicinal chemistry to push the boundaries of innovation.

DeepTech Recognition: AQEMIA is proud to be part of the French Tech 40 and France 2030, highlighting our role as a key player in Europe’s DeepTech ecosystem.

Prime Location with Flexibility: Our offices are located in the heart of Paris and London (King’s Cross), with flexible work arrangements including up to two remote days per week.

Strong Financial Backing: $100M raised from leading European and International investors

We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses and identifying potential inconsistencies or verification signals in application materials based on available information. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.