Senior Scientist, Binder Design and Development

Flagship Pioneering, Inc.•Cambridge, MA

About The Position

FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to transform the way these critical research, diagnostic, and therapeutic tools are manufactured. We are seeking a creative, motivated, and technically exceptional Senior Scientist to lead the design, development, and screening of peptide and protein-based binders targeting small-molecule substrates. This individual will build and scale high-throughput workflows for binder discovery, affinity characterization, and functional validation, playing a central role in shaping a novel molecular control platform. This is a rare opportunity to build foundational technology within a deeply integrated, fast-moving startup backed by Flagship’s venture creation engine. Position Summary Senior Scientist – Peptide & Protein Binder Design and Development The Senior Scientist will lead efforts to design, engineer, express, and characterize genetically encoded peptide and protein binders against defined small-molecule targets. This role spans the full discovery workflow, from scaffold selection and library design, to assay development, high-throughput expression, affinity screening, and hit-to-lead optimization. The ideal candidate is a hands-on protein/peptide engineer with deep expertise in binder discovery platforms and quantitative biophysical characterization. They are comfortable building scalable screening systems, handling large datasets, and iterating rapidly through design–build–test–learn (DBTL) cycles with machine learning / computational support.

Requirements

Ph.D. in Protein Engineering, Biochemistry, Structural Biology, Molecular Biology, or related discipline.
4+ years of relevant industry experience
Demonstrated experience in protein or peptide binder discovery and optimization.
Hands-on expertise in quantitative affinity screening (BLI, SPR, FP, ITC, or related technologies).
Experience designing and executing high-throughput screening workflows.
Strong understanding of protein-ligand interaction principles and binding thermodynamics.
Proven ability to run iterative design–build–test cycles in a fast-paced environment.

Responsibilities

Lead the design and engineering of peptide and protein-based binders targeting small-molecule substrates, leveraging rational design, library construction, and directed evolution strategies.
Build and execute high-throughput discovery and screening workflows, including display-based selection platforms and scalable expression systems capable of evaluating large variant libraries.
Develop and apply quantitative biophysical assays (e.g., BLI, SPR, FP, ITC) to generate affinity curves, determine kinetic parameters (kon/koff), calculate KD values, and establish selectivity profiles.
Drive iterative design–build–test–learn (DBTL) campaigns, integrating affinity and functional data with computational modeling to rapidly optimize binder performance.
Provide scientific and strategic leadership within the binder engineering workstream, contributing to IP development, cross-functional collaboration, and the establishment of a rigorous, high-velocity experimental culture.