Senior Director, API Development

Protagonist Therapeutics; Newark (CA); On-site; USD 245,000 - 280,000; Full time

Benefits offered by this job

Health Care benefits

401(k) Plan

Flexible Vacation Policy

Life Insurance (Basic, Voluntary & AD&

Disability coverage

Job summary

Protagonist Therapeutics is seeking an experienced API process research and development chemist to support route scouting, organic synthesis process development and scale up of peptide drugs. The successful candidate will manage the API group and coordinate scale up with CDMOs.

The role requires a PhD in synthetic organic chemistry and at least 15 years of process R&D experience in peptides and small molecules, with strong knowledge of FDA/ICH/cGMP guidelines and regulatory filings.

Qualifications

• Experience with DoE applied to process development.
• Familiar with FDA/ICH/cGMP guidance and regulatory expectations.
• Proven ability to lead cross-functional teams and manage projects.

Responsibilities

• Foster collaboration with Drug Discovery and Pre-clinical teams to develop scalable manufacturing routes for peptides and small molecules.
• Analyze data to evaluate synthesis routes for peptides using SPPS and LPPS.
• Communicate results clearly to internal and external teams to drive API development.
• Develop manufacturing and supply strategies with CDMOs to meet global regulatory expectations.
• Lead evaluation of third-party contractors and suppliers for process development and manufacturing.

Skills

DoE methods

Regulatory CMC filings

Project leadership

Analytical thinking

Education

PhD in synthetic organic chemistry

Job description

About Us

Protagonist Therapeutics is a biopharmaceutical company built on a proprietary peptide technology platform that has now produced two FDA‑approved, first‑in‑class medicines, generating royalties and milestones from global commercial partnerships with Johnson and Johnson and Takeda Pharmaceutical Company Limited. ICOTYDE™ (icotrokinra), licensed to Johnson & Johnson company Janssen Biotech, Inc., is the first and only targeted oral peptide that precisely blocks the Interleukin‑23 receptor. ICOTYDE was launched in the U.S. in March 2026 for the treatment of moderate‑to‑severe plaque psoriasis in adults and pediatric patients 12 years of age or older and is in Phase 3 development for psoriatic arthritis, ulcerative colitis and Crohn’s disease. ICOTYDE was jointly discovered by Protagonist and Johnson & Johnson scientists, with Protagonist having primary responsibility for the development of ICOTYDE through Phase 1, and Johnson & Johnson assuming responsibility for further clinical and regulatory development and commercialization. Protagonist also discovered and led research and development through Phase 3 for MIMRYLO™ (rusfertide), a first‑in‑class hepcidin mimetic peptide licensed to Takeda Pharmaceutical Company Limited for worldwide commercialization. MIMRYLO is approved in the U.S. for the treatment of erythrocytosis in adults with PV. The Company also has a number of clinical and preclinical programs based on clinically and commercially validated targets and addressing unmet medical needs, including an oral IL‑17 antagonist peptide, anti‑obesity dual and triple agonists, an oral hepcidin functional mimetic, and the recently announced IL‑4 and amylin discovery programs.

About Us

Protagonist Therapeutics is a biopharmaceutical company built on a proprietary peptide technology platform that has now produced two FDA‑approved, first‑in‑class medicines, generating royalties and milestones from global commercial partnerships with Johnson and Johnson and Takeda Pharmaceutical Company Limited. ICOTYDE™ (icotrokinra), licensed to Johnson & Johnson company Janssen Biotech, Inc., is the first and only targeted oral peptide that precisely blocks the Interleukin‑23 receptor. ICOTYDE was launched in the U.S. in March 2026 for the treatment of moderate‑to‑severe plaque psoriasis in adults and pediatric patients 12 years of age or older and is in Phase 3 development for psoriatic arthritis, ulcerative colitis and Crohn’s disease. ICOTYDE was jointly discovered by Protagonist and Johnson & Johnson scientists, with Protagonist having primary responsibility for the development of ICOTYDE through Phase 1, and Johnson & Johnson assuming responsibility for further clinical and regulatory development and commercialization. Protagonist also discovered and led research and development through Phase 3 for MIMRYLO™ (rusfertide), a first‑in‑class hepcidin mimetic peptide licensed to Takeda Pharmaceutical Company Limited for worldwide commercialization. MIMRYLO is approved in the U.S. for the treatment of erythrocytosis in adults with PV. The Company also has a number of clinical and preclinical programs based on clinically and commercially validated targets and addressing unmet medical needs, including an oral IL‑17 antagonist peptide, anti‑obesity dual and triple agonists, an oral hepcidin functional mimetic, and the recently announced IL‑4 and amylin discovery programs.
More information on Protagonist, its pipeline drug candidates, and clinical studies can be found on the Company's website at https://www.protagonist-inc.com.

Position Summary

Protagonist Therapeutics is seeking an experienced API process research and development chemist to support route scouting, organic synthesis process development and scale up of our synthetic peptide drugs. The successful candidate will handle chemical process research, large scale laboratory production and process and related technology transfer to CDMOs and management of partnering CDMOs. The candidate will be heading and managing the API group.

We are committed to a thriving in‑office culture. This role requires being on‑site at our office in Newark, CA 4 days a week.

Responsibilities

• Foster a collaborative culture interacting with Drug Discovery and Pre‑clinical Development team during preliminary stages of drug development. Analyze the first enabling procedures and develop phase‑appropriate routes to efficient and scalable manufacturing of peptides, non‑canonical amino acids and small molecules to support pre‑clinical and clinical trials.
• Use analysis of data to evaluate and compare chemicals syntheses using both Solid (SPPS) and Liquid‑Phase Peptide Synthesis (LPPS) for therapeutic peptides.
• Communicate results clearly and rapidly to internal and external teams to drive execution and delivery of APIs.
• Develop and execute manufacturing and supply strategies of raw materials, regulatory starting materials, and drug substances that meet global regulatory expectations. Work with multiple CDMOs in sourcing amino acids, peptide fragments for large scale manufacturing of APIs; effectively manage outsourced PR&D and production activities.
• Lead the evaluation and choice of global third‑party contractors and suppliers for process development and manufacturing activities.
• Collaborate closely with analytical scientists to monitor and understand the impact of process changes on the yield and impurity profile during development of peptide APIs.
• Interface between analytical and toxicology departments in identification and qualification of impurities. Contribute to Quality and CMC‑related regulatory correspondence.
• Maintain a current understanding of peptide and organic process R&D literature.
• Maintain a current understanding of global regulatory health care requirements, ICH and FDA guidelines, and filing strategy.
• Effectively document both laboratory and scale up activities.
• Take the initiative and actively drive creative and innovative solving of problems, both technical, managerial and timing.

Required Skills & Qualifications

• PhD in synthetic organic chemistry, with at least 15 years of process research and development experience in peptides and small molecules.
• Experience with DoE method applied to process development. Strong understanding of FDA/ICH/cGMP guidance.
• Demonstrated ability to effectively lead projects with internal and external resources.
• Experienced with regulatory CMC filings in IND, NDA, IMPD, PAS covering all phases of pre‑clinical and clinical development in both the US and global markets, knowledge of relevant FDA and EMA regulations and able to work within regulatory agency requirements.
• Analytical thinker and problem‑solver capable of identifying risks and risk mitigation strategies.
• Strong teamwork, negotiation and influencing skills, able to work in a team setting and establish clear and consistent goals and aims.
• Must be direct, detailed oriented, self‑driven and purposeful, and able to multi‑task to achieve results.
• Must be able to adhere to strict project timelines and budgets recommend teams and management on impacts and changes in project timelines.
• Inventive thinker, able to assess and take calculated risks to move project forward, and champion innovative ideas and approaches.

Pay Range

The base pay range for this position at commencement of employment is expected to be between $245,000 and $280,000/year; however, base pay offered may vary depending on multiple individualized factors, including market location, job‑related knowledge, skills, and experience.

Benefits

A top priority for Protagonist Therapeutics, Inc. is to provide a robust and comprehensive health and wellness program for our employees and their families. We offer a variety of high‑quality coverage and benefit options.

• Health Care benefits. Protagonist covers 100% of the premium cost for medical, dental, and vision coverage for all full‑time employees and their dependents.
• Flexible Spending Accounts – Healthcare FSA, Dependent Care FSA, Commuter Benefits
• 401(k) Plan
• Flexible Vacation Policy
• Life Insurance (Basic, Voluntary & AD&D)
• Short Term & Long Term Disability
• Company paid lunch and snacks