Director/Senior Director, Computational Chemistry

Flagship Pioneering, Inc.•Cambridge, MA

12d•$176,000 - $294,300

About The Position

Flagship Labs 111 Inc. (FL111), an early-stage biotechnology company developing therapeutic modalities through innovations in chemistry, computation, and data science, is seeking a Director/Senior Director of Computational Chemistry. This strategic leadership role will spearhead the design and optimization of heterobifunctional small molecules and shape computational strategy across the company’s portfolio. The role partners closely with medicinal chemists, structural biologists, and project teams to build and apply computational tools that guide molecular design across the design–build–test–learn cycle. The successful candidate will drive molecular ideation, property optimization, and compound prioritization; advance computational modeling and cheminformatics capabilities; and build and mentor a high-performing computational chemistry function. The position is based in Cambridge, Massachusetts. The required background is a PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline, with at least 10 years of relevant industry experience, including scientific leadership and people management. Experience with heterobifunctional small molecules, ADME optimization for large flexible molecules, and an early-stage or startup biotech environment is preferred.

Requirements

PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline.
At least 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 binary and ternary settings, with a record of driving impactful decisions across multiple drug discovery programs.
Ability to drive and evaluate real, synthetically actionable molecular designs.
Experience using cheminformatics tools for compound design, analysis, and prioritization.
Demonstrated scientific leadership and communication skills, including the ability to lead interdisciplinary teams and influence senior stakeholders.

Nice To Haves

Prior experience working on heterobifunctional small molecules, such as PROTACs.
Familiarity with ADME optimization challenges for large, flexible molecules.
Prior experience in an early-stage or startup biotech environment.

Responsibilities

Define the strategic vision for and lead design of heterobifunctional small molecules, including ligand selection, attachment vectors, and linker architectures, integrating cross-functional input to balance target engagement, molecular properties, and synthetic efficiency.
Lead cheminformatics strategy to identify and prioritize chemical series, and oversee development of internal computational workflows and data infrastructure.
Direct assessment of molecular properties such as solubility, permeability, lipophilicity, and clearance risk, and lead compound-prioritization frameworks that integrate developability across the portfolio.
Advance structure-based and AI/ML-assisted modeling capabilities, including docking, conformational analysis, and FEP, to inform ligand selection, attachment strategy, and linker design; promote adoption of emerging computational methods.
Partner strategically with chemistry, biology, and in vivo pharmacology teams; align on portfolio priorities; and represent computational chemistry in leadership discussions and external scientific forums.
Build, lead, inspire, mentor, and develop computational chemistry scientists and interdisciplinary teams.