Director/Senior Director, Computational Chemistry at Flagship Pioneering, Inc.

About the role
Flagship Labs 111 Inc. (FL111) is actively seeking a highly experienced Director or Senior Director of Computational Chemistry to lead the design, development, and application of computational strategies for heterobifunctional small molecules. This leadership role involves collaborating closely with medicinal chemists, structural biologists, and other scientific teams to create computational tools and workflows that will inform and accelerate molecular design processes throughout the drug discovery pipeline. The successful candidate will play a critical role in guiding molecular ideation, optimizing key properties such as solubility and permeability, and prioritizing compounds across multiple projects to ensure efficient progression toward therapeutic candidates. This position offers an opportunity to influence early-stage biotech research at a strategic level, shaping the future of novel molecule development within a dynamic and innovative environment. Key facts

Location:
Cambridge, MA Engagement: Full-time The role reports to the leadership of the Computational Chemistry Team, working within a multidisciplinary environment that integrates chemistry, biology, pharmacology, and data science to advance drug discovery efforts. The position involves on-site work at the Cambridge, MA office, with no mention of remote or hybrid arrangements. The role requires a leader capable of managing complex projects and guiding scientific teams in a rapid-paced biotech setting. The company offers a competitive salary range and benefits package aligned with industry standards for senior scientific leadership roles.

What you'll do
- Develop and execute the strategic vision for designing heterobifunctional small molecules,



including PROTACs and other bifunctional modalities, focusing on ligand selection, linker architecture, and attachment points that optimize target engagement while maintaining drug-like properties.
- Lead the creation and refinement of computational workflows, including cheminformatics pipelines, to identify promising chemical series and facilitate compound prioritization based on predicted activity, developability, and synthetic feasibility.
- Oversee the assessment of key molecular properties such as solubility, permeability, stability, and other ADME-related parameters, and develop frameworks to incorporate these factors into compound ranking and decision-making processes.
- Drive the adoption and enhancement of structure-based drug design approaches, including molecular docking, modeling, and AI/ML techniques, to inform ligand and linker design, and advocate for innovative computational methods to improve efficiency and accuracy.
- Collaborate closely with medicinal chemists, structural biologists, and in vivo pharmacologists to ensure computational strategies are aligned with experimental efforts, and serve as a scientific partner in project planning, data interpretation, and decision-making.
- Lead efforts to develop and implement computational tools that support the entire research cycle, from initial molecular design to candidate optimization, ensuring seamless integration with laboratory workflows.




- Mentor and develop a team of computational chemists and data scientists, fostering a culture of scientific excellence, innovation, and continuous learning.
- Represent the computational chemistry function in leadership meetings, external conferences, and publications, promoting the company's scientific achievements and strategic vision.
- Stay current with advances in computational chemistry, cheminformatics, and related fields, and evaluate current technologies and methodologies for potential application within the organization.
- Manage project timelines, budgets, and resource allocation to ensure timely delivery of computational solutions that meet project goals and organizational standards. Requirements
- PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline, with a minimum of 10 years of industry experience in drug discovery or related fields, including proven leadership and management capabilities.
- Extensive expertise in computational medicinal chemistry, structure-based drug design, and cheminformatics, with a track record of influencing and advancing drug discovery programs.
- Demonstrated ability to generate innovative molecular designs, evaluate compound properties, and mentor scientists in computational techniques.
- Proficiency with cheminformatics platforms, molecular modeling software, docking tools, and data analysis/visualization programs.
- Solid leadership skills, with experience managing interdisciplinary teams and influencing senior stakeholders across research functions.
- Knowledge of heterobifunctional molecules such as PROTACs, with an understanding of their unique design considerations and challenges.
- Familiarity with ADME optimization challe

📌 Director/Senior Director, Computational Chemistry (Town of Cambridge)
🏢 Flagship Pioneering
📍 Town of Cambridge