FL| Cambridge, MA Director, Medicinal Chemistry

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies to transform health care and sustainability?

At Flagship Labs 107 (FL107), a Flagship Pioneering-backed stealth biotechnology company, we’re pioneering the mastery of protein control: tuning the stability, degradation, and localization, of any protein. By systematically rewriting the rules of protein homeostasis, we’re on a mission to target the “undruggable” and treat the “impossible.” Our innovative approach combines novel biology, medicinal chemistry, and AI/ML-powered molecular design, all driven by our unwavering commitment to dramatically improve patient lives.

As we advance our platform and progress toward the clinic, we are seeking an exceptional Director of Medicinal Chemistry to lead small molecule discovery efforts across multiple programs. This is a foundational scientific leadership role, ideal for a medicinal chemist who combines scientific rigor, creative drive, and operational acumen to advance first-in-class therapeutics from concept to IND.

Reporting to our SVP, Research, the Director of Medicinal Chemistry will establish medicinal chemistry competencies at FL107, working across discovery programs. You will help lead the design and execution of small molecule discovery campaigns at the core of the platform, leveraging DNA-encoded library (DEL) and covalent fragment screening, AI/ML-driven generative chemistry, and structure-based design. Your goal will be to help identify and create novel protein modulators, including heterobifunctional degraders, molecular glues, and other proximity-inducing molecules.

You will collaborate closely with biology, computational, and biochemistry teams to integrate new chemo types into our drug discovery efforts, while managing external chemistry partnerships. This is a unique opportunity to define FL107’s chemistry strategy, build the execution engine, and help shape the platform and portfolio of a high-growth company from the ground up.

• Lead medicinal chemistry activities and strategy across multiple early discovery programs through conception to DC nomination and IND-enabling activities.
• Drive and design optimization of compounds identified by DEL screening, covalent fragment discovery, and structure/AI-guided approaches.
• Define and prioritize medicinal chemistry workflows to enable exploration of proximity-inducing modalities such as molecular glues and heterobifunctional molecules.
• Serve as chemistry lead across cross-functional teams, providing deep insight into SAR, PK/PD, potency, and drug-like properties.
• Build and manage a highly productive network of CRO partners, ensuring timely execution of synthesis, hit-to-lead, and scale-up activities.
• Partner with computational scientists to iterate on predictive models and generative design strategies; evaluate and apply in silico compound generation tools.
• Contribute to and help shape FL107’s intellectual property strategy around novel chemical matter and mechanisms.
• Design, build, and oversee FL107’s compound data infrastructure to ensure high-quality, well-curated datasets that power structure-based drug design (SBDD) and machine learning initiatives.
• Provide leadership, mentorship, and technical direction to a growing internal chemistry team as FL107 scales.

• PhD in Organic or Medicinal Chemistry with experience in small molecule drug discovery.
• Proven track record advancing multiple programs through hit-to-lead and lead optimization; experience nominating development candidates is essential.
• Demonstrated success working with emerging modalities (e.g., molecular glues, bifunctional molecules, induced proximity) and complex scaffolds.
• Deep understanding of structure-based drug design, SAR optimization, and balancing key parameters (potency, ADME/PK, physicochemical properties).
• Comfortable partnering with AI/ML teams and evaluating computational and generative design inputs/outputs.
• Experience managing distributed CRO teams, external synthesis workflows, and global chemistry partnerships.
• Strong…