About Abiologics 

Abiologics is a Flagship Pioneering company developing Synteins™ — a transformative class of fully synthetic proteins composed entirely of artificial building blocks such as D-amino acids and non-canonical residues. SynteinsTM are designed to transcend the limitations of traditional biologics, with improved oral stability, immune evasion, and metabolic durability — all while being fully programmable by design. 

Powered by a proprietary AI-enabled discovery platform, Abiologics integrates generative design, automated synthesis, and rapid experimental screening to enable iterative optimization at scale. 

Position Summary 

We are seeking a Protein Design Scientist to join the Computational Protein Design team and help drive structure-based design and optimization of synthetic proteins. This is a highly interdisciplinary role at the interface of computational design, structural biology, and protein engineering. 

Ideal candidates have deep experience in de novo protein design, miniproteins, and binders engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment. 

Key Responsibilities 

• Design and execute SynteinsTM engineering campaigns to generate drug candidates. 
• Create computational design strategies to deliver drug candidates drawing from array of ML tools and Rosetta scripts. 
• Collaborate with computation, chemistry, and experimental biology teams to optimize designs for function, solubility, and stability. 
• Integrate structural and biophysical data (e.g., binding, CD, HDX-MS, CryoEM) into iterative optimization cycles 

Qualifications 

Required 

• PhD in structural biology, biophysics, protein design, or related field 
• 2+ years of hands-on experience in structure-guided protein design 
• Demonstrated proficiency with modern structure prediction and design tools such as RFdiffusion, proteinMPNN, AF2, Boltz2, BoltzGen, Rosetta or equivalent SOTA tools for in-silico protein engineering. 
• Strong understanding of the biophysics of protein folding and interface energetics 
• Demonstrated ability to progress designs from concept to experimental testing 
• Excellent communication skills  

Preferred 

• Experience designing minibinders or proteins <100 AAs 
• Familiarity with non-canonical amino acid design 
• Familiarity with molecular dynamics tools. 
• Exposure to high-throughput or automated protein engineering environments 
• Prior work on platform-based or early-stage biotech teams 

Why Join Abiologics 

• Help invent a new class of programmable synthetic proteins 
• Be part of a high-velocity discovery platform with real-time synthesis and screening 
• Collaborate with a deeply interdisciplinary, mission-driven team 
• Redefine the limits of what proteins can do 

ABOUT FLAGSHIP PIONEERING:

The salary range for this role is $146,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Abiologics, Inc currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc's good faith estimate as of the date of publication and may be modified in the future.

COMPANY DESCRIPTION

Abiologics, Inc. is a privately held, early-stage biotechnology company on a mission to make biology better through an innovative therapeutic modality. We are pioneering the development of Synteins™, a transformational class of macromolecular medicines unlocked by novel synthetic and computational technologies. Abiologics is actively seeking exceptional scientists who are passionate about driving therapeutic modality innovation in biotechnology.

Abiologics was founded in Flagship Pioneering’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA) and Generate Biomedicines were conceived and created. Since Flagship’s founding in 2000, the firm has originated and fostered the development of more than 100 scientific ventures resulting in more than 500 issued patents and more than 50 clinical trials for novel therapeutic agents.

THE ROLE

We are seeking an experienced and motivated Senior Scientist in Medicinal Chemistry specializing in miniprotein and peptide drugs. The successful candidate will lead projects in designing, synthesizing, and optimizing novel miniprotein therapeutics called Synteins™. This role offers a unique opportunity to bring a new drug modality from early-stage research through to clinical development.

KEY RESPONSIBILITIES

• Independently plan, execute, interpret, and optimize Syntein structure-activity campaigns through direct, hands-on laboratory work.
• Implement modern peptide chemistry and conjugation methodologies to accelerate optimization of miniprotein drug development.
• Collaborate with cross-functional teams including computational chemistry, biology, and pharmacology to drive project success.
• Drive bench-side innovation, ensuring that ideas transition seamlessly from concept to reality
• Mentor and guide junior scientists, fostering a collaborative and dynamic laboratory environment.
• Contribute to patent applications and scientific publications, showcasing lab innovation.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Ph.D. (with a minimum of 5 years of industry experience) or M.S. (with a minimum of 12 years of industry experience) in Medicinal Chemistry, Synthetic Organic Chemistry, Chemical Biology, or related field
• Strong track record of laboratory-based innovation and problem-solving in drug discovery including optimization of affinity, selectivity, drug properties, and PK profile.
• Proven expertise in the hands-on peptide synthesis.
• Ability to lead and inspire a team of scientists in a dynamic research setting.
• Excellent communication skills for both technical and non-technical audiences.
• Able to work on-site and attend in-person meetings.

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. Abiologics, Inc currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc’s good faith estimate as of the date of publication and may be modified in the future.