Director/Senior Director, Computational Chemistry

COMPANY DESCRIPTION Flagship Labs 111 Inc. (FL111) is a privately held, early-stage biotechnology company pioneering a novel platform harnessing innovations in chemistry, computation, and data science to create new therapeutic modalities beyond traditional small molecules. FL111 is backed by Flagship Pioneering, bringing the courage, vision, and resources to guide FL111 from platform validation to patient impact. We are seeking collaborative, creative and relentless problem solvers that share our passion for impact to join us! THE ROLE 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. KEY 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, integrating cross-functional input to balance target engagement, molecular properties, and synthetic efficiency across programs. Cheminformatics & Library Exploration: Lead and direct cheminformatics strategy to identify and prioritize chemical series; oversee development of internal computational workflows and data infrastructure to support program needs ADME & Developability Assessment: 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. Structure-Based & Computational Modeling: 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. Cross-Functional Collaboration: 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. PROFESSIONAL EXPERIENCE & QUALIFICATIONS PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline, with 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. 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. Location: Cambridge, MA About Flagship Pioneering Flagship Pioneering is a bioplatform innovation company that invents and b…