Director, Protein Engineering

Winnow Therapeutics is a VC-backed, next-generation immunotherapy company focused on transforming the treatment of autoimmune diseases. Founded by world-renowned scientific leaders and supported by top-tier investors, we are advancing a new class of medicines aimed at restoring immune balance and redefining outcomes for patients with autoimmune conditions. By combining proven science with innovative approaches, we aim to deliver deep and lasting responses.

We are building our founding team in Boston, Massachusetts, offering a unique opportunity to join at an early stage to help shape the future of the company. ABOUT THE ROLE Winnow is seeking a strategic and innovative Director, Protein Engineering to drive the design and optimization of next-generation T-cell engager biologics for the treatment of autoimmune diseases. This role will shape our protein engineering strategy, advance our molecular engineering capabilities, and play a central role in building and evolving a world-class discovery organization.

The successful candidate will bring scientific vision, organizational leadership, and strong cross-functional partnership to generate differentiated immune-modulating molecules from discovery through preclinical development. This is a ‘player-coach role’ for a scientist who is energized by both setting technical strategy and rolling up their sleeves to advance our science. This is an ideal opportunity for a scientist who thrives at the intersection of strategy, innovation, and team development.

You will influence critical molecular engineering decisions that determine candidate success, including format architecture, anti-CD3 arm selection and tuning, affinity and specificity engineering, and developability optimization, while helping to guide the broader scientific direction of our immunology portfolio. RESPONSIBILITIES Drive protein engineering strategy for bispecific antibodies and T-cell engager programs targeting autoimmune disease, advancing molecular design, optimization, and characterization efforts including affinity tuning, specificity engineering, stability optimization, and developability assessment Oversee design and execution of antibody engineering campaigns using display technologies, structure-guided design, and modern computational and AI/ML approaches; integrate emerging tools into the workflow to create real engineering leverage Guide selection and optimization of antibody formats, linker architectures, Fc engineering strategies, and half-life extension approaches Establish the biophysical characterization strategies for lead selection, including binding kinetics, thermal and colloidal stability and aggregation Manage external CROs and research collaborators supporting engineering, expression, purification and characterization activities Partner closely with immunology, translational, pharmacology, and CMC teams to advance candidates toward IND-enabling studies Support intellectual property strategy, invention disclosures, and scientific publications/presentations Contribute to diligence activities, partnering discussions, and investor presentations as a scientific leader Help build a culture that embraces scientific excellence and continuous learning to increase our team’s ability to deliver novel drug development opportunities through rapid incorporation of emerging biotechniques on the leading-edge of biologics drug discovery. QUALIFICATIONS Ph.D. in Protein Engineering, Biochemistry, Immunology, Structural Biology, or related field 10+ years of industry experience in antibody/protein engineering, including leadership experience in biotech or pharma Demonstrated expertise in bispecific antibodies, T-cell engagers, or multi-specific biologics required, with expertise with Fc engineering, developability assessment, and manufacturability optimization preferred Experience advancing biologics candidates from discovery into preclinical development required; experience contributing to IND submissions or clinical-stage biologics programs preferred Experience in autoimmune disease therapeutics or immune modulation preferred Working fluency with modern computational and AI/ML approaches to protein engineering with the judgement to deploy them productively Prior experience in a venture-backed or early-stage biotech environment a plus SKILLS & COMPETENCIES Impactful leadership skills and demonstrated ability to contribute to a foundational capability Excellent analytical, problem solving and critical thinking skills, including an ability to combine attention to detail with a big picture perspective Strong oral and written communication skills with experience presenting across all levels of the organization Ability to thrive in a fast-paced, innovative, and evolving environment while remaining flexible, proactive, and resourceful Adept at prioritizing and managing multiple tasks simultaneously, integrating cross-functional collaboration and balancing competing priorities effectively Collaborative and team-oriented mindset with a desire to positively impact a new company’s evolving culture Winnow Therapeutics is an equal opportunity employer , providing equal opportunities to all employees and applicants for employment without regard to race, color, religion, sex or gender identity, national origin, age, disability, sexual orientation or genetics.

In addition to federal law requirements, Winnow Therapeutics complies with applicable state and local laws governing nondiscrimination in employment. #J-18808-Ljbffr