Senior Director, Computational Chemistry & Molecule Design

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 176,000 - 294,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Other benefits

Job summary

Flagship Labs 111 Inc. (FL111) seeks a Director/Senior Director, Computational Chemistry to lead design and optimization of heterobifunctional small molecules. You will guide molecular design, develop computational workflows, and drive developability strategies across multiple programs.

The successful candidate will shape computational strategy, mentor a world-class team, and partner with multidisciplinary groups to accelerate patient-impact projects in Cambridge, MA.

Qualifications

• PhD in Chemistry or related field with 10+ years of industry experience and leadership.
• Deep expertise in computational medicinal chemistry and structure-based drug design.
• Experience guiding heterobifunctional small molecules (PROTACs) programs is preferred.
• Strong ability to mentor scientists and influence senior stakeholders.
• Familiarity with ADME optimization for large, flexible molecules is preferred.

Responsibilities

• Define strategic vision for the computational chemistry function and drive design of heterobifunctional small molecules.
• Lead cheminformatics strategy and build internal computational workflows and data infrastructure.
• Direct ADME/developability assessment and lead compound prioritization frameworks.
• Champion structure-based and AI/ML modeling to inform ligand design and linker architecture.
• Collaborate across chemistry, biology, and in vivo pharmacology to align portfolio priorities.

Skills

Computational medicinal chemistry

Structure-based drug design

Molecular design leadership

Cross-functional collaboration

Mentoring scientists

Heterobifunctional molecules (PROTACs)

Education

PhD in Chemistry, Medicinal Chemistry, Computational Chemistry

Tools

Cheminformatics tools

AI/ML modeling tools

Job description

Flagship Labs 111 Inc. (FL111) seeks a Director/Senior Director, Computational Chemistry to lead design and optimization of heterobifunctional small molecules. You will guide molecular design, develop computational workflows, and drive developability strategies across multiple programs.

The successful candidate will shape computational strategy, mentor a world-class team, and partner with multidisciplinary groups to accelerate patient-impact projects in Cambridge, MA.