Senior Director Protein Engineering Jobs (NOW HIRING)

Description

 About Aragen Bioscience

Aragen Bioscience is a leading contract research organization (CRO) dedicated to accelerating biologics discovery and development. Our capabilities span antibody discovery, protein engineering, cell line development, process development, and analytical characterization. We partner with emerging biotechnology companies and global pharmaceutical organizations to advance innovative therapies from concept to clinic.

We are seeking a highly motivated Scientist/Senior Scientist, Protein Sciences & Biologics Development to lead client programs, mentor scientific staff, and drive the development of next-generation biologic therapeutics. This is a hands-on scientific leadership role combining technical excellence, client engagement, and people leadership in a fast-paced CRO environment.

Position Summary

The Senior Scientist will serve as a technical lead for client-sponsored biologics programs, overseeing activities from molecular design and protein engineering through expression, purification, characterization, and technology transfer. The successful candidate will provide scientific leadership to project teams, contribute to business growth through exceptional client delivery, and coach junior scientists while maintaining hands-on laboratory involvement.

This position requires extensive experience in protein sciences, molecular biology, protein engineering, and downstream process development, together with a demonstrated ability to lead multiple client programs simultaneously. Due to the time-sensitive nature of projects and critical experimental workflows, occasional evening and weekend work may be required. 

Key ResponsibilitiesScientific Leadership & Client Delivery

• Lead and manage client-sponsored biologics development programs from concept through deliverable completion.
• Serve as the primary scientific contact for assigned clients, providing technical guidance, project updates, risk assessment, and strategic recommendations.
• Present scientific data, project milestones, and development strategies to internal and external stakeholders.
• Mentor and develop scientists, research associates, and junior team members through technical coaching and career development support.
• Drive project execution to ensure delivery of high-quality data packages, reports, and client deliverables within established timelines.
• Author and review technical reports, SOPs, study protocols, technical transfer documentation, and regulatory-supporting data packages.
• Collaborate with multidisciplinary teams to resolve complex scientific and operational challenges.
• Contribute to department innovation, workflow improvements, and scientific best practices.

Biologics Discovery & Molecular Biology

• Design and optimize expression constructs and mammalian expression vectors for recombinant protein production.
• Utilize AI-enabled and computational tools to support protein engineering, sequence optimization, structural prediction, and developability assessments.
• Perform and oversee molecular biology workflows including: 
  • Gibson Assembly
  • Restriction enzyme cloning
  • Site-directed mutagenesis
  • Plasmid characterization
  • Sequence verification
• Lead RNA and DNA analytical workflows, including qPCR and RT-qPCR applications.
• Apply bioinformatics tools for sequence analysis, codon optimization, construct design, and genetic engineering strategies.

Protein Engineering & Developability

• Lead protein engineering, sequence optimization, and developability assessments for therapeutic proteins.
• Evaluate protein stability, aggregation propensity, solubility, manufacturability, and biophysical properties.
• Support antibody engineering, Mult specific formats, fusion proteins, cytokines, protein scaffolds, and other next-generation biologic modalities.
• Collaborate with clients to develop strategies for candidate optimization and risk mitigation.

Protein Expression & Purification

• Design, execute, and optimize recombinant protein expression workflows.
• Lead hands-on downstream purification activities utilizing automated FPLC systems such as AKTA Avant and AKTA Pure.
• Develop and optimize purification processes using: 
  • Affinity Chromatography
  • Ion Exchange Chromatography (IEX)
  • Size Exclusion Chromatography (SEC)
  • Hydrophobic Interaction Chromatography (HIC)
• Support process development and scale-up activities including: 
  • Depth filtration
  • Tangential Flow Filtration (TFF)
  • Ultrafiltration/Diafiltration (UF/DF)
• Troubleshoot complex purification and expression challenges independently.

Requirements

Required Qualifications

Education & Experience

• Ph.D. in Molecular Biology, Biochemistry, Protein Engineering, Biotechnology, Chemical Engineering, or a related scientific discipline with 7+ years of relevant industry experience, OR
• M.S. in a related scientific discipline with 12+ years of relevant industry experience.
• Demonstrated experience in a CRO, biotechnology, or pharmaceutical environment.
• Proven track record of leading external client projects and delivering successful outcomes.
• Minimum 2 years of direct people leadership, mentoring, or supervisory experience.

Technical Expertise

• Strong expertise in molecular biology, cloning technologies, vector design, and recombinant protein expression.
• Extensive experience in protein engineering, developability assessment, and sequence optimization.
• Deep hands-on experience in downstream process development and protein purification using FPLC systems.
• Strong understanding of protein characterization, stability, aggregation, and formulation considerations.
• Familiarity with computational biology, structural modeling, or AI-enabled protein engineering tools.
• Experience with electronic laboratory notebooks (ELNs), scientific data analysis, and laboratory automation platforms.

Leadership & Professional Skills

• Exceptional written and verbal communication skills.
• Strong client-facing presentation and relationship management capabilities.
• Ability to manage multiple complex projects simultaneously in a deadline-driven environment.
• Demonstrated strategic thinking, scientific problem-solving, and decision-making skills.
• Strong mentoring, coaching, and team-development abilities.

Preferred Qualifications

• Experience with antibody engineering, Mult specific antibodies, fusion proteins, cytokines, and alternative protein scaffolds.
• Experience supporting technology transfer and manufacturing scale-up activities.
• Familiarity with GMP environments and regulatory expectations.
• Experience implementing AI-enabled scientific workflows for protein design and development.

Why Join Aragen?

• Work with cutting-edge biologics programs across diverse therapeutic modalities.
• Collaborate with innovative biotech startups and leading global pharmaceutical companies.
• Shape the scientific direction of client programs while mentoring the next generation of scientists.
• Join a collaborative and entrepreneurial environment focused on scientific excellence and client success.

Aragen Bioscience is an Equal Opportunity Employer.