Senior Scientist, Binder Design and Development

What if…you could pioneer a new approach to designing life's most essential molecules?

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 Scientistto 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.

Key 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.

Qualifications

Ph.D. in Protein Engineering, Biochemistry, Structural Biology, Molecular Biology, or related discipline.