Associate Director/Director, Medicinal Chemistry

Flagship Pioneering, Inc.•Cambridge, MA

11d

About The Position

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 an experienced and highly innovative AD/D, 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.

Requirements

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

Responsibilities

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.