FL| Cambridge, MA Associate Director​/Director, Medicinal Chemistry

Associate Director/Director, Medicinal Chemistry

Cambridge, MA USA

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!

FL111 is seeking an experienced and highly innovative Associate Director/Director of Medicinal Chemistry to lead chemistry efforts for small‑molecule drug discovery programs. This role will drive medicinal chemistry strategy from hit identification through lead optimization and candidate selection, working closely with biology, DMPK, computational chemistry, and FSP partners. The ideal candidate is a hands‑on scientific leader with deep medicinal chemistry expertise, with a track record of delivering on small molecule heterobifunctional and/or induced proximity programs.

• Design and implement medicinal chemistry strategies from early discovery through candidate selection, leveraging structure‑ and property‑based design principles.
• Drive compound design and optimization by integrating SAR, ADME/DMPK, pharmacology, and safety data to meet target product profiles.
• Partner with computational chemistry teams to apply computational approaches to molecular design and optimization.
• Manage and direct external CRO partnerships, including oversight of complex synthetic routes, timelines, data quality, and compound delivery and registry.
• Collaborate with biology teams to interpret data and guide decision‑making in a continuous and iterative design, synthesize, test, learn loop.
• Collaborate with legal and IP teams to draft, review, and support patent filings related to medicinal chemistry innovations.

• PhD. in Organic Chemistry or Medicinal Chemistry with 8-10+ years of industry experience in small molecule drug discovery within a pharma or biotech environment.
• Track record of delivering on small molecule heterobifunctional and/or induced proximity programs (e.g., PROTACs).
• Deep expertise in medicinal chemistry, including synthetic organic chemistry, SAR analysis, ADME, pharmacokinetics, and drug design principles.
• Proven ability to lead projects and cross‑functional team.
• Excellent communication skills with the ability to convey complex scientific concepts.
• Experience managing external CROs and contributing as a chemistry leader.

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID‑19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at

Flagship Pioneering is 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.

Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other…