Associate Director, Protein Sciences

Aera Therapeutics Inc.; Cambridge (MA); On-site; USD 180,000 - 200,000; Full time

Benefits offered by this job

Annual bonus

Equity incentives

Health insurance

401k with match

Paid time off

Commuting reimbursement

Job summary

Aera Therapeutics is seeking an Associate Director of Protein Sciences in Cambridge, MA, to lead production and evaluation of targeting moieties for LNPs and AOCs. You will manage a six-person team, partner across R&D functions, and ensure robust, scalable antibody-related processes.

The role requires on-site presence at least 4 days/week. You will drive site-specific conjugation strategies, oversee CRO/CDMO relationships, and advance GMP manufacturing readiness while balancing program timelines

Qualifications

• PhD or equivalent with 8+ years in industry (or MS/BS with 12+ years).
• 3+ years of direct people management, building high-performing teams.
• Hands-on recombinant antibody expression and purification in mammalian systems.
• Bioconjugation of antibodies/fragments using site-specific chemistries.
• Protein analytics including SEC, CE-SDS, intact mass spec, HIC/DAR determination.
• Experience managing CROs/CDMOs and tech transfer toward GMP manufacturing.
• Strong cross-functional collaboration and communication skills.
• Experience with AOCs/ADCs or ligand-targeted nanoparticles preferred.
• Familiarity with IND-enabling activities and CMC knowledge.

Responsibilities

• Lead and grow a team of six scientists, setting direction and recruiting as the group scales.
• Serve as protein sciences lead on cross-functional program teams, collaborating with LNP, Therapeutic Discovery, in vivo pharmacology, and CMC.
• Oversee production and purification of antibodies and fragments across research and scale-up.
• Lead conjugation strategy and optimization for AOCs, including chemistry and DAR evaluation.
• Own external protein sciences portfolio, CRO/CDMO selection, scope and budget management, and tech transfer for GMP production.
• Develop material forecasts and supply plans; identify risks and reallocate resources.
• Drive AOC platform development with binder screening and protein engineering efforts (humanization, affinity maturation).
• Present results to senior leadership and participate in strategy discussions and partnerships.

Skills

People management

Antibody expression & purification

Bioconjugation chemistry

Protein analytics

GMP/IND readiness

Cross-functional collaboration

AOC/ADC expertise

Protein engineering

Computational protein design

Regulatory documentation

Education

PhD in biochemistry, protein science, chemical biology, or related field

Tools

Mammalian expression platforms

SEC / IEX / HIC analytics

SPR/BLI binding assays

Job description

Aera Therapeutics was founded by a world-class team of scientists, investors, and company builders with a shared vision to unlock the potential of genetic medicines across a broad range of modalities and therapeutic areas. We strive for excellence and an industry-leading position in our chosen delivery platforms, while aggressively hunting for opportunities where enabling delivery technologies can unlock applications of high, unmet medical need.

Leveraging deep expertise in the space, Aera has a leading lipid nanoparticle (LNP) platform that enables today’s applications, while investing in and developing a potentially disruptive antibody oligonucleotide conjugate (AOC) platform to enable tomorrow’s applications.

How will your role make an impact at Aera Therapeutics?

As Associate Director of Protein Sciences, you will lead the effort on production and evaluation of our targeting moieties for our LNPs and AOCs. Your responsibilities will include managing a team of scientists to work cross functionally to further develop our AOC platform, as well as supporting the construct production needs for our therapeutic programs. You will be reporting to the Senior Director of Delivery Technologies and will be expected to be on site at least 4 days a week.

You will:

• Lead and grow a team of six scientists, setting technical direction, mentoring and developing team members, and recruiting talent as the group scales
• Serve as the protein sciences lead on cross-functional program teams, partnering with LNP formulation, Therapeutic Discovery , in vivo pharmacology, and CMC to make recommendations, define material needs, and deliver against program timelines
• Oversee production and purification of antibodies and antibody fragments (e.g., mAb, Fab, scFv, and VHH) across research and scale-up, ensuring robust, reproducible processes and timely supply
• Lead conjugation strategy and execution for AOCs, including selecting and optimizing conjugation chemistries and characterizing conjugates for identity, purity, DAR/ligand density, and functional activity
• Own the external protein sciences portfolio, including CRO/CDMO selection, scope and budget management, data review, and tech transfer to enable GMP production
• Develop and maintain material forecasts and supply plans across programs, proactively identifying risks and making resourcing tradeoffs
• Drive AOC platform development, including screening and evaluation of novel binders and constructs and protein engineering efforts (e.g., humanization, affinity maturation), balanced against program delivery priorities
• Present results, plans, and recommendations to senior leadership, and contribute to internal strategy discussions, external partnerships, and regulatory documentation as needed

Qualifications:

• PhD in biochemistry, protein science, chemical biology, or a related field with 8+ years of relevant industry experience, or MS/BS with 12+ years
• 3+ years of direct people management, with a track record of building, developing, and leading high-performing scientific teams
• Deep hands-on expertise in recombinant antibody and antibody fragment expression with mammalian systems and purification (e.g., affinity, IEX, SEC, HIC) across multiple scales
• Demonstrated expertise in bioconjugation to antibodies and fragments using site‑specific chemistries
• Strong grounding in protein and conjugate analytics (e.g., SEC, CE‑SDS, intact mass spec, HIC/DAR determination) and binding assays (e.g., SPR/BLI)
• Proven experience managing CROs/CDMOs and leading tech transfer toward GMP manufacturing
• Excellent communication and cross‑functional collaboration skills, with the ability to prioritize across competing programs in a fast‑paced environment
• Experience with AOCs, ADCs, or ligand‑targeted nanoparticles is preferred
• Protein engineering experience, including humanization, affinity maturation, and developability assessment
• Familiarity with computational protein design tools
• Working knowledge of CMC requirements and IND‑enabling activities is preferred
• Commitment to our Core Values: Respect, Integrity, Excellence, Impact

The approximate salary range for this role is $180,000- $200,000

Our salary ranges are determined by job scope, level, and location. The range displayed on this job posting reflects the minimum and maximum target for new hire salaries for the position as posted. Within the range, individual pay is determined by a variety of factors, including job‑related skills, experience, relevant education or training, and business need. In addition to the base salary, eligible employees will have an opportunity to participate in an annual cash bonus, equity incentives, and a robust benefits offering that includes health insurance, 401k retirement plan with company match, paid sick and vacation time, life and disability insurance, and commuting expense reimbursement.

Aera Therapeutics is an Equal Opportunity Employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex (including pregnancy, sexual orientation, or gender identity), national origin, age, disability, protected veteran status, genetic information, or any other characteristic protected by applicable federal, state, or local law.