Senior Scientist Analytical Development & Quality Control

Senior Scientist Analytical Development & Quality Control

Protagonist Therapeutics is seeking a talented and highly motivated Senior Scientist to join the Analytical Development & Quality Control (ADQC) group. The successful candidate will help drive analytical development strategy for small-molecule and peptide candidates from early development through late-stage programs, including analytical method development, validation, transfer, stability programs, phase-appropriate specifications, and analytical control strategies for drug substance (DS) and drug product (DP). This role includes leading internal analytical activities, managing external CDMO partners, and collaborating closely with Drug Substance, Drug Product, Supply Chain, Quality Assurance, Regulatory, Nonclinical, and Clinical teams to achieve program objectives. This position reports to the Senior Director of ADQC.

Responsibilities

• Develop, optimize, and validate analytical methods for release, stability, and characterization testing of DS and DP.
• Lead impurity identification, degradant analysis, comparability assessments, method transfer, and analytical method lifecycle management.
• Establish phase-appropriate, scientifically robust analytical control strategies, including characterization plans and specification setting, to support clinical and regulatory requirements and enable accelerated development timelines.
• Troubleshoot analytical issues and support investigations, including OOS/OOT results, deviations, root-cause analysis, CAPA recommendations, and change-control activities, as applicable.
• Manage stability and reference standard programs for assigned projects.
• Communicate effectively with stakeholders and manage analytical development and QC testing activities at CDMOs.
• Review CDMO data for release testing, stability testing, and DS/DP characterization to ensure scientific rigor, data integrity, and compliance.
• Author analytical sections for regulatory filings, including INDs, IMPDs, and NDAs, and provide input to relevant Module 3 sections.
• Participate in continuous improvement initiatives, including process and workflow improvements, CDMO management practices, and SOP development or revision in collaboration with Quality Assurance.
• Represent ADQC in cross-functional team meetings.

Qualifications

• PhD or MS in Analytical Chemistry or a relevant scientific discipline, with 5+ years of experience supporting early- and late-stage CMC development.
• Hands-on expertise in UHPLC method development using a range of detection technologies, including UV, PDA, MALS, CAD, conductivity, fluorescence, and advanced MS for identification and structural characterization.
• Extensive experience developing analytical methods for synthetic peptides or similarly complex drug substance molecules, such as ADCs, PEGylated proteins, or monoclonal antibodies, is highly preferred.
• Demonstrated ability to solve complex scientific and business challenges.
• Extensive experience communicating with and managing analytical development and QC functions at CDMOs.
• Strong knowledge of cGMP/GLP compliance, pharmaceutical quality systems, and regulatory requirements for drug development.
• Excellent written and verbal communication skills, with the ability to effectively represent analytical development plans to CDMOs, internal project teams, CMC teams, and senior management.
• Ability to manage priorities and maintain timelines in a fast-paced environment while balancing speed, quality, and risk.
• Strong project management, communication, leadership, and cross-functional collaboration skills.
• Experience in small- to mid-size innovator companies is desired.
• Ability to travel domestically and internationally, as needed.

The base pay range for this position at commencement of employment is expected to be between $140K and $160K / year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.

Protagonist Therapeutics is a discovery through late-stage development biopharmaceutical company. The Company''s proprietary peptide technology platform enables de novo discovery of peptide therapeutics. Two novel peptides derived from Protagonist''s proprietary discovery platform are at or near commercialization. ICOTYDE (icotrokinra) is approved in the U.S. for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age and older who weigh at least 40 kg who are candidates for systemic therapy or phototherapy. ICOTYDE is the first and only targeted oral peptide that precisely blocks the Interleukin-23 receptor (IL-23R) licensed to Janssen Biotech, Inc.,a Johnson & Johnson company. 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 development and commercialization. An NDA for rusfertide, a first-in-class hepcidin mimetic peptide that is being co-developed with Takeda Pharmaceuticals pursuant to a worldwide license and collaboration agreement entered in 2024, is under priority review with the FDA. Protagonist holds an option to co-commercialize rusfertide in the U.S. through a 50/50 profit and loss share structure or can opt-out of this structure. The Company also has a number of preclinical stage drug discovery programs addressing clinically and commercially validated targets including an oral IL-17 peptide antagonist, obesity dual and triple agonists, an oral hepcidin functional mimetic, and the recently announced IL-4 and amylin 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.