Senior Computational Chemist

Aqemia; Paris; Hybrid; EUR 120,000 - 180,000; Full time

Benefits offered by this job

Flexible work arrangement (up to 2 rem

Paris and London offices

Job summary

AQEMIA in Paris and London is seeking a high-impact scientist to drive computer-aided design of novel small molecules. You will integrate physics-based modeling, generative AI, and medicinal chemistry to guide decisions across internal programs and pharma partnerships.

You will work with chemists, biologists, physicists, and ML scientists to push early drug discovery from hit identification to candidate nomination, while evolving AI-assisted design methods and workflows.

Qualifications

• PhD or Master's with strong industry depth in drug discovery.
• Experience in small molecule design across hit-to-lead and lead optimization.
• Proficiency in Python and Linux; ability to run and adapt computational workflows.

Responsibilities

• Design, prioritize and optimize small molecules across programs.
• Own the design hypothesis and adapt plans as data evolves.
• Apply docking, MD, free energy methods and chemoinformatics in design decisions.
• Integrate biochemical, biophysical and ADME-Tox data to guide experiments.
• Pilot new AI-enabled design workflows within live projects.

Skills

Structure-based design

Ligand-based design

Protein-ligand interactions

Python scripting

Linux

Evidence-driven communication

Education

PhD in computational chemistry/medicinal chemistry/chemical biology/biophysics or related field

Master’s in a relevant field with equivalent industry depth

Tools

RDKit

OpenMM

AmberTools

GROMACS

Job description

About AQEMIA

AQEMIA is a drug invention company dedicated to creating entirely new medicines to address major unmet medical needs. At the core of our mission is QEMI, our proprietary molecule-invention platform, which uniquely combines cutting-edge science with advanced technology. Powered by physics-based modeling, statistical mechanics, and generative AI, QEMI allows our teams to design novel drug candidates from first principles. What makes AQEMIA different is our commitment to true innovation: our research is dedicated to the invention of new molecular entities, not the refinement of existing ones. We focus on inventing never-before-seen molecules, without relying on experimental data, and advancing them into a growing pipeline of proprietary programs and strategic partnerships with leading pharmaceutical companies. Our most advanced preclinical programs are currently in vivo optimization, targeting diseases still waiting for effective treatments, offering our teams the opportunity to work on science that can make a real difference in people’s lives. For more information, visit AQEMIA.com, our WTTJ Page, and our LinkedIn.

About Our Team

AQEMIA brings together a diverse, multidisciplinary team of 80+ professionals based in Paris and London. Our scientists and engineers, including chemists, physicists, machine learning experts, and software engineers, work side by side to push the boundaries of early-stage drug discovery. This close collaboration across disciplines is central to our approach, enabling us to tackle complex scientific challenges from first principles and translate cutting-edge ideas into novel therapeutic candidates. At AQEMIA, team members are encouraged to contribute their expertise, learn from one another, and play an active role in shaping the future of drug invention.

About The Drug Discovery Team

The Drug Discovery Sciences team combines expertise in medicinal chemistry, computational chemistry, biology, and translational science. Working at the intersection of AI-driven drug design, molecular simulations, and experimental science, the team is responsible for driving scientific excellence across Aqemia’s drug discovery programs and delivering clinical candidates. They develop and apply innovative methodologies ensuring that scientific insights translate into high-quality therapeutic opportunities. Partnering closely with Platform, Engineering, and Program teams, they play a critical role in advancing novel small-molecule therapeutics from concept to clinical candidate.

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

Nice-to-Have

• Writing your own Python scripts and tools, and using AI coding assistants to speed up analysis and workflow building
• Experience with generative AI for molecular design, AI agents, or automated design-make-test-analyze workflows
• Experience as an application scientist at a computational drug discovery software provider, supporting real discovery projects
• Exposure to diverse target classes and to drug discovery partnerships with pharma collaborators
• Familiarity with multi-parameter optimization and ADME-Tox prediction

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.