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 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, quantitative affinity screening, and rigorous kinetic characterization, 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 Discovery and Biophysical Characterization (Small molecules)

The Senior Scientist will lead efforts to design, engineer, express, and characterize peptide and protein binders against defined small-molecule targets. This role spans the full discovery workflow, with a particular emphasis on designing robust, quantitative assays to measure peptide–small molecule interactions, including development of high-throughput screening methods and rigorous kinetic characterization (kon/koff, KD).

The candidate will play a central role in establishing assay strategies that distinguish true binding from nonspecific or electrostatic interactions, particularly for challenging, low-molecular-weight and highly charged substrates. This role includes building scalable screening workflows, integrating fluorescence-based assays with label-free kinetic methods, and driving iterative design–build–test–learn (DBTL) cycles.

The ideal candidate is a hands-on experimentalist with deep expertise in biophysical assay development and molecular interaction characterization, comfortable building new measurement systems from first principles and interpreting complex, artifact-prone datasets.

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 (e.g., FP, TR-FRET) and, where appropriate, display-based selection platforms, capable of evaluating large variant libraries.
• Design, build, and optimize biophysical assays for peptide–small molecule interactions, with careful attention to signal-to-noise, assay window, and physicochemical confounders.
• Develop and apply quantitative biophysical assays (e.g., BLI, FP, TR-FRET, SPR, GCI, ITC) to determine binding affinity and kinetics (kon, koff, KD), including selection of appropriate assay formats for low-molecular-weight, highly charged ligands.
• Establish and implement counterscreens and control strategies to distinguish specific binding from nonspecific electrostatic or phosphate-driven interactions.
• Collaborate with external CROs and core facilities for advanced kinetic measurements (e.g., SPR/GCI), while owning assay design, data interpretation, and iterative experimental strategy internally.
• 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

• PhD. in Protein Engineering, Biochemistry, Structural Biology, Molecular Biology, or related discipline.
• 5+ years of relevant industry experience
• Demonstrated experience in protein or peptide binder discovery and optimization.
• Hands-on expertise in designing and troubleshooting quantitative binding assays, including fluorescence-based methods (FP, TR-FRET) and/or label-free biosensors (BLI, SPR, GCI), with demonstrated ability to generate reliable kinetic and affinity measurements.
• Experience working with small-molecule ligands (<1 kDa) or other low-signal binding systems, including strategies to improve assay sensitivity and specificity.
• Demonstrated ability to identify and resolve biophysical assay artifacts (e.g., nonspecific binding, aggregation, electrostatic effects, mass transport limitations).
• Experience designing and executing high-throughput screening workflows.
• Strong understanding of protein–ligand interaction principles, binding thermodynamics, and kinetics.
• Proven ability to run iterative design–build–test cycles in a fast-paced environment.
• Experience working with nucleotide or phosphate-containing ligands is a plus.

Who You Are

• Innovative Pioneer: You thrive in breaking new ground scientifically and are passionate about leveraging protein biochemistry to create transformative technologies.
• Collaborative Contributor: You excel in cross-functional teams, readily share expertise, and value the input of colleagues.
• Inventive Problem Solver: You proactively identify challenges and rapidly ideate creative solutions.
• Mission-Driven Individual: You are driven by an ambition to fundamentally change how biomolecules are synthesized and to meaningfully impact human health and biotechnology.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, generating billions in value. Flagship companies are known for addressing humanity’s most pressing challenges and advancing innovative solutions with global impact.

We are an equal opportunity employer and are dedicated to building diverse and inclusive teams. If you have some of the qualifications listed above but not all, we still encourage you to apply. We value passion, experience in many forms, and unique backgrounds.

Come pioneer the future with us.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto. 

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL116 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL116's good faith estimate as of the date of publication and may be modified in the future.