Director, Medicinal Chemistry

Protagonist Therapeutics; Newark (CA); On-site; USD 195,000 - 235,000; Full time

Job summary

Protagonist Therapeutics Inc. in Newark, CA is seeking a Director of Medicinal Chemistry to lead a team in small molecule and peptide drug discovery.

The role focuses on hit-to-IND strategies, SAR optimization, and cross-functional collaboration within a fast-paced environment on-site four days a week. The ideal candidate has a PhD with 10+ years in drug discovery, proven leadership, and strong experience with ADME/PK and analytical techniques such as HPLC/LC-MS.

Qualifications

• Ph.D. in Synthetic Organic Chemistry or Medicinal Chemistry.
• 10+ years of drug discovery experience in pharma/biotech.
• Experience leading medicinal chemistry teams.
• Proven record in synthesis, medicinal chemistry, and analytical techniques.
• Experience with computational and structural biology in drug discovery.
• Track record of leading early discovery projects and identifying development candidates.
• Experience coordinating with cross-functional teams and CROs.

Responsibilities

• Lead and manage a medicinal chemistry group and external CROs to support multiple programs.
• Design and execute medicinal chemistry strategies from hit/lead to development candidates.
• Co-lead discovery programs and develop work plans to IND-ready candidates.
• Develop SAR and multi-parameter optimization for high-quality candidates.
• Plan internal/external resources including computational/structural inputs.
• Communicate with cross-functional teams and senior management.
• Evaluate CROs and oversee preclinical chemistry activities.

Skills

Medicinal chemistry

Drug discovery

Leadership

CRO management

ADME/PK

Synthesis chemistry

SAR analysis

HPLC/LC-MS

Cross-functional work

Computational chemistry

Structural biology

Education

Ph.D. in Synthetic Organic Chemistry or Medicinal Chemistry

Tools

Computational chemistry

Structural biology

Job description

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

The Discovery Chemistry team at Protagonist Therapeutics is seeking a highly motivated and experienced Director of Medicinal Chemistry to lead and manage a competent chemistry group in small molecule and peptide drug discovery against a diverse range of therapeutic targets. The individual will be responsible for the design and execution of efficient medicinal chemistry strategies in hit/lead discovery, lead optimization, as well as development candidate progression and nomination for first-in-human clinical studies. The individual will lead the design, synthesis, and structure-activity-relationship analysis of new molecules, and solve challenging problems with critical thinking within our multi-disciplinary drug discovery team. The individual will also effectively manage external chemistry resources and seamlessly integrate them with internal expertise to ensure high overall chemistry productivity. The individual will have a demonstrated track record in synthetic organic chemistry and medicinal chemistry, and is highly enthusiastic about drug discovery. The individual will co-lead multiple discovery programs, and possess effective interpersonal skills, as well as excellent verbal and written communication capabilities. Exact role ranges from Associate Director, Director, to Sr. Director of Medicinal Chemistry depending on experience, and will report to VP of Chemistry.
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

• Lead and manage a competent medicinal chemistry group and external chemistry resources to support multiple small molecule and peptide drug discovery programs.
• Responsible for the design and execution of efficient medicinal chemistry strategies that drive the drug discovery process – including hit/lead discovery and lead optimization, ADME/PK, pharmacology, and toxicology - to successfully deliver development candidates into first-in-human clinical studies.
• Co-lead multiple drug discovery programs against diverse therapeutic targets and provide functional expertise and input in the development of work plans from lead identification to clinical development candidate selection.
• Develop structure-activity relationships and conduct multi-parameter optimization to identify high-quality drug candidates.
• Effectively plan for and prioritize internal and external medicinal chemistry resources to achieve project goals including the use of computational and structural resources.
• Communicate, collaborate, and coordinate effectively with cross-functional teams.
• Effectively communicate project work, issues, schedules, and accomplishments to senior management.
• Evaluate and select chemistry CROs and oversee key preclinical chemistry activities.

Required Skills & Qualifications

• Ph.D. in Synthetic Organic Chemistry or Medicinal Chemistry
• 10+ years of drug discovery experience in a pharmaceutical and/or biotechnology setting as a medicinal chemist
• Experience in leading and managing medicinal chemistry teams
• Demonstrated capabilities and working knowledge of synthetic chemistry, medicinal chemistry, and analytical techniques as evidenced by a record of achievement (publications, patents, etc.). Experience with the use of computational and structural biology during the drug discovery process
• Demonstrated track record of leading/managing early discovery projects and identifying development candidates against challenging targets with a deep understanding of both hit and lead generation and lead optimization
• Experience in working efficiently within a strong, multi-disciplinary team and utilizing cross-functional information, such as ADME/PK, in vitro assays, and in vivo pharmacology to drive drug design and optimization strategies
• Experience in managing diverse and multiple CROs for medicinal chemistry and biological evaluations
• A strong understanding of the pharmacology, DMPK and toxicology requirements of oral and injectable therapeutics
• Experience in the supervision, mentoring, and development of other scientists
• Proficient in analyzing data, and addressing technical challenges using analytical and problem-solving skills
• Solid understanding of Intellectual property in drug discovery and attention to detail when involved in the drafting of patent applications
• Excellent working knowledge of critical analytical and separations technologies, such as HPLC, RP-HPLC, LC/MS, ion exchange and size-exclusion chromatography, and the ability to evaluate new technologies
• Enthusiastic self-starter with strong organizational and interpersonal skills
• Demonstrated ability to successfully thrive in a dynamic, fast-paced, innovative environment with an emphasis on teamwork, collaboration, and communication within team and across the departments

Pay Range

The base pay range for this position at commencement of employment is expected to be between $195,000 and $235,000/year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.

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)