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Director/Senior Director, Computational Chemistry

Flagship Pioneering, Inc. Cambridge, Сполучені Штати
On-site work

Publication date: 12/11/2026

FL111 is seeking a Director/Senior Director, Computational Chemistry to spearhead the design and optimization of heterobifunctional small molecules. This leader will work closely with medicinal chemists, structural biologists, and project teams to develop and apply computational tools to guide molecular design decisions across the design–build–test–learn cycle. The successful candidate will drive molecular ideation, property optimization, and compound prioritization across the portfolio. This is a strategic, high-impact leadership role where the Director/Senior Director will shape computational strategy, drive scientific excellence, and help build and mentor a world-class computational chemistry function.

Responsibilities

Molecular Design & Optimization: Define the strategic vision for and drive the design of heterobifunctional small molecules, including ligand selection, attachment vectors, and linker architectures; Cheminformatics & Library Exploration: Lead and direct cheminformatics strategy to identify and prioritize chemical series; oversee development of internal computational workflows and data infrastructure; ADME & Developability Assessment: Direct evaluation of key molecular properties (e.g., solubility, permeability, lipophilicity, clearance risk) and lead compound prioritization frameworks; Structure-Based & Computational Modeling: Champion and advance structure-based and AI/ML-assisted modeling capabilities (e.g., docking, conformational analysis, FEP) and drive adoption of emerging computational methods; Cross-Functional Collaboration: Serve as a strategic scientific partner and computational chemistry leader across chemistry, biology, and in vivo pharmacology teams, and represent the computational chemistry function in leadership discussions and external scientific forums

Requirements

PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline; 10+ years of relevant industry experience, including demonstrated scientific leadership and people management experience; Deep expertise in computational medicinal chemistry and structure-based drug design in the binary and ternary settings, with a track record of driving impactful decisions across multiple drug discovery programs; Demonstrated ability to drive and evaluate real, synthetically actionable molecular designs and to mentor and develop scientists to do the same; Experience using cheminformatics tools for compound design, analysis and prioritization; Proven scientific leadership and communication skills: demonstrated ability to build, lead, and inspire interdisciplinary teams and influence senior stakeholders

Nice to have

Prior experience working on heterobifunctional small molecules (e.g., PROTACs); Familiarity with ADME optimization challenges for large, flexible molecules; Prior experience in an early-stage or startup biotech environment

Benefits

Healthcare coverage; annual incentive program; retirement benefits; broad range of other benefits
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