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, 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. 

• 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. 

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.