Principal Scientist, Protein Engineering

Xairatherapeutics; South San Francisco (CA); On-site; USD 164,000 - 205,000; Full time

Job summary

Xaira Therapeutics in the San Francisco Bay Area is seeking a Principal Scientist to lead AI-driven protein engineering for therapeutic proteins and antibodies. You will design, produce, and characterize molecules, guiding experimental strategies and collaborating with computational designers.

You will mentor junior staff, oversee CROs, and drive program strategy from conception through early discovery with a hands-on, on-site leadership role in a fast-paced startup environment.

Qualifications

• Ph.D. in molecular biology/biochemistry/structural biology or related field.
• 6+ years in biotech/biopharma R&D with large-molecule programs.
• Hands-on protein engineering with antibodies and proteins.
• Experience with developability and stability studies.

Responsibilities

• Define scientific strategy for therapeutic programs with AI-driven discovery.
• Collaborate with AI designers to guide design campaigns.
• Lead binder discovery and prioritize screening strategies.
• Develop strategies to optimize binder affinity and developability.
• Present progress to cross-functional teams.
• Design, produce, purify, and characterize therapeutic proteins and antibodies.
• Maintain accurate ELN records and contribute to reports.
• Ensure lab safety and efficient operations.
• Mentor junior staff and oversee CROs.
• Help define Protein Engineering portfolio with leadership.

Skills

Protein engineering

Antibody formats

Developability assessments

Structure prediction tools

Mentoring

Education

Ph.D. in relevant field

Tools

PyMOL

AlphaFold

Job description

About Xaira Therapeutics

Xaira is an innovative biotech startup focused on leveraging AI to transform drug discovery and development. The company is leading the development of generative AI models to design protein and antibody therapeutics, enabling the creation of medicines against historically hard-to-drug molecular targets. It is also developing foundation models for biology and disease to enable better target elucidation and patient stratification. Collectively, these technologies aim to continually enable the identification of novel therapies and to improve success in drug development. Xaira is headquartered in the San Francisco Bay Area, Seattle, and London.

About the Role

As a member of the Protein Engineering team at Xaira, you will play a critical role in the AI-driven discovery and development of protein therapeutics, integrating experimental protein engineering with computational design.

As a Principal Scientist, you will provide scientific and technical leadership from program conception through early discovery and lead optimization. You will partner closely with computational protein designers to guide AI-driven design campaigns and develop experimental strategies to evaluate designed molecules. You will engineer, produce, and characterize therapeutic proteins and antibodies, with an emphasis on optimizing functional properties and developability.

The ideal candidate will bring deep technical expertise in protein engineering, a strong understanding of antibody formats and developability metrics, and a demonstrated ability to guide scientific strategy and mentor junior staff. This is a hands‑on, lab‑based, on‑site position with significant program leadership responsibilities.

Responsibilities

• Define the scientific strategy for one or more therapeutic programs in partnership with the Disease Biology and Therapeutic Protein Design teams. Contribute to the evaluation of novel targets, define therapeutic hypotheses and target product profiles, and develop integrated, AI‑driven drug discovery strategies.
• Work closely with computational protein designers to identify relevant structural and biological features of therapeutic targets and incorporate these insights into design campaigns.
• Lead binder discovery campaigns, working closely with internal teams to prioritize screening strategies, interpret results, and identify hits.
• Collaborate with protein designers to develop and execute strategies to optimize binder affinity, specificity, and developability.
• Serve as a scientific lead in cross‑functional program meetings, communicating protein engineering strategy and progress to internal stakeholders
• Design, produce, purify, and characterize therapeutic proteins, including antibodies, using chromatographic techniques and biophysical and biochemical assays..
• Maintain accurate, timely, and complete experimental records in an electronic laboratory notebook (ELN).
• Contribute to the preparation of technical reports, regulatory documentation, and scientific presentations.
• Ensure compliance with laboratory safety protocols and contribute to laboratory organization and operational efficiency.
• Stay current with advances in antibody engineering and protein design, and apply these insights to help shape the team’s scientific direction.
• Mentor and develop junior scientific staff, supporting a high‑performing, collaborative team.
• Oversee CROs supporting outsourced work, ensuring data quality and timely delivery.
• Help define and prioritize the Protein Engineering team’s project portfolio in collaboration with leadership.

Qualifications

• Ph.D. in a relevant scientific discipline, with a strong foundation in molecular biology, biochemistry, structural biology, or a related field.
• At least 6 years of industry experience in biotech or biopharma R&D supporting large‑molecule therapeutic programs.
• Extensive hands‑on experience in protein engineering, including structural and functional characterization of antibodies and other proteins using advanced analytical methods.
• Deep expertise in antibody formats, production, purification, and characterization.
• Proficiency in developability assessments and stability studies.
• Proficiency with protein visualization and structure prediction tools, such as PyMOL and AlphaFold.
• Strong organizational, communication, and interpersonal skills.
• Ability to propose novel scientific approaches and a strong interest in exploring relevant therapeutic hypotheses.
• A proactive, self‑directed approach, with excellent problem‑solving and troubleshooting skills.
• Enthusiasm for working in a fast‑paced, collaborative startup environment, with a demonstrated ability to promote cooperation and knowledge sharing across multidisciplinary teams.
• A strong record of scientific achievement, demonstrated by first‑author publications in peer‑reviewed journals or granted patents.

• Direct experience with structure prediction or machine learning tools for protein design is preferred.
• Experience collaborating with Process Development and supporting IND documentation is nice to have.

Compensation

Annual

We offer a competitive compensation and benefits package, seeking to provide an open, flexible, and friendly work environment to empower employees and provide them with a platform to develop their long‑term careers. A Summary of Benefits is available for all applicants. We offer a competitive package that includes base salary, bonus, and equity. The base pay range for this position is expected to be $164,000 to $205,000 annually; however, the base pay offered may vary depending on the market, job‑related knowledge, skills and capabilities, and experience.

Xaira Therapeutics an equal‑opportunity employer. We believe that our strength is in our differences. Our goal to build a diverse and inclusive team began on day one, and it will never end.