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 fast-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 new 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.
Strong 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 challenges, particularly for large and flexible molecules, is highly desirable.
Experience working in a startup or early-stage biotech environment is preferred, demonstrating adaptability and a proactive approach.
Excellent communication skills, capable of translating complex computational concepts into actionable insights for diverse audiences.
Ability to manage multiple projects simultaneously, prioritize tasks effectively, and deliver results within tight timelines.
Nice to have
Experience applying machine learning and artificial intelligence techniques to drug design and discovery.
Familiarity with high-throughput screening methods and data integration approaches.
Knowledge of synthetic chemistry considerations relevant to complex, large molecules.
Prior involvement in early-stage biotech or startup environments, demonstrating agility and entrepreneurial spirit.
Skills & tools
Proficiency in computational chemistry software such as Schrödinger, MOE, or equivalent platforms.
Experience with cheminformatics tools like Pipeline Pilot, KNIME, or similar data analysis platforms.
Familiarity with molecular docking, molecular dynamics, and simulation tools.
Ability to analyze large datasets, generate visualizations, and communicate findings effectively to multidisciplinary teams.
Knowledge of programming languages such as Python, R, or similar for data analysis and automation tasks is a plus.
Practical notes
The salary range for this position is between $176,000 and $294,300, with the final figure determined based on the candidate's experience, skills, and qualifications.
The company offers comprehensive healthcare coverage, an annual incentive program, retirement benefits, and other benefits as part of its total compensation package.
All salary and benefits information provided are estimates as of the posting date and are subject to change.
This role is based on-site in Cambridge, MA, and requires physical presence at the office.
Flagship Pioneering is committed to fostering an inclusive setting and encourages candidates from diverse backgrounds to apply.
If you possess some of the listed qualifications but not all, your application is still welcomed, as skills are transferable, and enthusiasm is valued.
Unsolicited resumes from staffing agencies are not accepted unless directly engaged by Flagship Pioneering's internal Talent Acquisition team.
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📌 Director/Senior Director, Computational Chemistry (Hobart)
🏢 Flagship Pioneering
📍 Hobart