Director/Senior Director, Computational Chemistry

Flagship Pioneering•Cambridge, MA

11h

About The Position

Flagship Labs 111 Inc. (FL111), a privately held, early-stage biotechnology company backed by Flagship Pioneering, is developing a platform that combines chemistry, computation, and data science to create therapeutic modalities beyond traditional small molecules. FL111 seeks a Director/Senior Director, Computational Chemistry to lead the design and optimization of heterobifunctional small molecules. The role partners with medicinal chemists, structural biologists, and project teams to develop 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 across the portfolio; shape computational strategy and scientific standards; and build and mentor the computational chemistry function. The position is located in Cambridge, Massachusetts.

Requirements

PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline.
10 or more years of relevant industry experience.
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.
Strong scientific leadership and communication skills, including the ability to build, lead, and inspire 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 across programs.
Lead cheminformatics strategy to identify and prioritize chemical series, and oversee development of internal computational workflows and data infrastructure.
Direct evaluation of molecular properties such as solubility, permeability, lipophilicity, and clearance risk, and lead compound prioritization frameworks that integrate developability considerations 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.
Act as a strategic scientific partner and computational chemistry leader across chemistry, biology, and in vivo pharmacology teams; align on portfolio priorities and represent the function in leadership discussions and external scientific forums.
Build, lead, mentor, and develop computational chemistry scientists and teams.