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.

Position Summary:

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 chemotypes 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.

Key Responsibilities:

• 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.

Required Qualifications

• PhD. in Organic or Medicinal Chemistry 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 cross-functional collaboration skills; fluent in communicating with biology, DMPK, IP, and data science stakeholders.
• Strategic mindset with strong scientific judgment, organizational leadership, and a drive to move with urgency.

• Excellent communication and synthesis skills, with the ability to present structured updates on complex scientific concepts to technical, non-technical, and executive audiences.

• Strong analytical skills with the ability to interpret complex datasets and derive meaningful insights.
• Proven ability to work effectively in a collaborative team environment and manage multiple projects simultaneously.
• Resourceful problem solver and self-starter.

Preferred Qualifications

• Experience with DEL screening, covalent chemistries, or reactive fragment libraries.
• Familiarity with designing bifunctional compounds, linker exploration, and ternary complex modeling.
• Prior experience in building and growing chemistry teams in a start-up or entrepreneurial environment.
• Strong IP and patent experience; comfort working with legal teams to develop and protect novel chemical matter.
• Exposure to platform-based discovery environments with multi-program pipelines.

What We Offer:

• Opportunity to lay the scientific foundation of a transformative platform company as an early employee, and to serve as a key contributor to the development of new technologies in the protein degradation field.

• Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
• Weekly lunches, monthly social events, and community lunchroom with free snacks, cold brew coffee tap, and a vibrant community with scientists and entrepreneurs.
• A collaborative and inclusive work environment that values diversity and innovation.
• Access to state-of-the-art facilities and cutting-edge technologies.

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, we encourage you to apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

The salary range for this role is $179,000 - $236,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL107 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL107's good faith estimate as of the date of publication and may be modified in the future.