Director/Senior Director, Computational Chemistry

Flagship Pioneering, Inc.•Cambridge, MA

5d•$176,000 - $294,300•Onsite

About The Position

Flagship Labs 111 Inc. (FL111) is an early-stage biotechnology company focused on creating new therapeutic modalities beyond traditional small molecules by leveraging innovations in chemistry, computation, and data science. Backed by Flagship Pioneering, FL111 is seeking a Director/Senior Director, Computational Chemistry to lead the design and optimization of heterobifunctional small molecules. This role involves close collaboration with medicinal chemists, structural biologists, and project teams to apply computational tools throughout the drug discovery cycle. The successful candidate will drive molecular ideation, property optimization, and compound prioritization, shaping the computational strategy and building a world-class computational chemistry function.

Requirements

PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline.
10+ years of relevant industry experience.
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 Haves

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

Responsibilities

Define the strategic vision for and drive the 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 and direct cheminformatics strategy to identify and prioritize chemical series; oversee development of internal computational workflows and data infrastructure to support program needs.
Direct evaluation of key molecular properties (e.g., solubility, permeability, lipophilicity, clearance risk) and lead compound prioritization frameworks that systematically integrate developability considerations across the portfolio.
Champion and advance structure-based and AI/ML-assisted modeling capabilities (e.g., docking, conformational analysis, FEP) to inform ligand selection, attachment strategy, and linker design; drive adoption of emerging computational methods across the organization.
Serve as a strategic scientific partner and computational chemistry leader across chemistry, biology, and in vivo pharmacology teams within the company; align on portfolio priorities, and represent the computational chemistry function in leadership discussions and external scientific forums.