Senior Director, Regulatory Affairs/CMC

Protego focuses on the discovery and development of first-in-class small molecule therapeutics that aim to reprogram protein folding for the treatment of various diseases. We are exploring monogenic protein misfolding diseases that cause myopathy, cardiomyopathy, stroke, renal disease, retinal diseases, channelopathies, and various degenerative diseases. Our approach builds on the proven pharmacological chaperones approach previously exemplified by tafamidis, which was discovered and developed by our cofounders Dr. Jeffery W. Kelly and Dr. Richard Labaudinière, for the treatment of transthyretin amyloidosis. About the job Protego Therapeutics is seeking an experienced Senior Director, Regulatory Affairs (CMC) to join our small regulatory team. Reporting to the Senior Vice President of Regulatory Affairs, the Senior Director will own and execute the global CMC regulatory strategy as the company advances its lead AL amyloidosis program from proof-of-concept directly into a global pivotal study and on toward NDA/MAA submission. This is a senior, hands-on role requiring deep small molecule CMC regulatory expertise and the judgment to operate as the company’s primary CMC regulatory voice with FDA and other global health authorities. The successful candidate will be equal parts strategist, author, and operator — setting the CMC regulatory strategy, personally driving submissions, managing CDMO and consultant partners, and building the CMC regulatory infrastructure that will carry the program through registration and beyond. Primary Responsibilities CMC Regulatory Strategy & Health Authority Engagement Own and execute the integrated global CMC regulatory strategy for Protego’s lead AL amyloidosis asset across proof-of-concept, pivotal, and registration phases, ensuring CMC readiness is never the rate-limiting step on the path to patients. Serve as Protego’s senior CMC regulatory point of contact with FDA and ex-US health authorities (EMA, MHRA, PMDA & NMPA), leading preparation, strategy, and delivery of Type B/C meetings, scientific advice, pre-NDA/pre-MAA interactions, and ad hoc agency engagements on CMC topics. Develop and execute strategies that leverage rare disease and expedited regulatory pathways — Orphan Drug Designation, Fast Track, Breakthrough Therapy, PRIME, and equivalent ex-US designations — to compress timelines without compromising data integrity. Anticipate CMC regulatory risk across the program (control strategy, starting material designation, impurity strategy, comparability, stability commitments, process validation strategy) and partner with the SVP and executive leadership to make informed, risk-balanced decisions. Provide CMC regulatory input into the target product profile (TPP) and integrated development plan. CMC Submissions & Documentation Lead and personally author/oversee authoring of CMC content (Modules 2.3 and 3) for INDs, IND amendments, CTAs/IMPDs, briefing books, annual reports, DSURs, orphan drug applications, and ultimately the NDA and MAA filings in eCTD format. Drive seamless proof-of-concept-to-pivotal CMC strategy, including phase-appropriate specifications, comparability protocols, process validation strategy, and registration stability program design. Coordinate and author CMC sections of agency briefing packages, designation applications, and responses to information requests. Establish and maintain a single source of truth for CMC submission content, ensuring consistency across regions and submission types as the program scales toward registration. Cross-Functional Collaboration Partner with the CMC team, Quality, Analytical Development, Clinical, Nonclinical, and Program Management to align development plans, timelines, and risk-mitigation strategies with global CMC regulatory expectations. Provide senior regulatory input on CMC development decisions, including drug substance and drug product process development, scale-up, tech transfer, analytical method development and validation, container/closure, and lifecycle planning. Review and provide CMC regulatory input on clinical protocols, investigator brochures (IBs), and IND/CTA-supporting documentation. Influence and align with the SVP and executive leadership on CMC regulatory matters that have material program or financial impact. Vendor, CDMO & Consultant Management Provide regulatory oversight of CDMO partners (drug substance, drug product, packaging, analytical testing), ensure their documentation, change control, and regulatory commitments are fit for purpose for a registrational program. Build a vendor and partner ecosystem that gives Protego the leverage of a larger organization while preserving the speed of a small one. Build out the CMC regulatory function commensurate with program growth — define and implement SOPs, document templates, regulatory intelligence processes, and submission planning tools fit for a pivotal- and NDA-ready company. Mentor and develop CMC regulatory talent (internal hires and/or embedded consultants) as the program scales. Maintain current knowledge of global CMC regulations and guidance (FDA, EMA, ICH Q1–Q14, USP / Ph. Eur. compendial changes) and translate intelligence into actionable program decisions. Maintain CMC regulatory files and archives to inspection-ready standards. Required Education, Experience, Skills, And Abilities Bachelor’s degree or higher in Chemistry, Pharmaceutical Sciences, Chemical Engineering, or a related scientific discipline; advanced degree (MS, PhD, PharmD) strongly preferred. 12+ years of progressive Regulatory Affairs experience with a strong and demonstrated focus on CMC for small molecules in biotech or pharmaceutical environments, including senior-level leadership (Director or above). Proven track record authoring and leading CMC components of INDs, CTAs, and at least one NDA or MAA submission, including direct authoring of Module 3 content. Direct experience leading CMC-focused FDA interactions (Type B/C meetings, pre-NDA meetings, written responses to information requests). Deep working knowledge of global CMC regulatory frameworks — FDA, EMA, ICH (Q1–Q14) — and a working understanding of major ex-US markets. Demonstrated experience in small, lean biotech environments, ideally including a program that transitioned from early clinical development through pivotal trial and toward registration. Strong technical fluency across small molecule drug substance and drug product development, analytical sciences, process validation, and control strategy. Experience managing CDMOs and external regulatory/CMC consultants as the operational backbone of a virtual or hybrid CMC organization. Preferred Qualifications Direct experience with rare disease, orphan drug, or expedited program development (Orphan Drug Designation, Fast Track, Breakthrough Therapy, PRIME). Prior experience supporting a single-asset or near-single-asset company through a pivotal / registrational inflection point. Experience in AL amyloidosis, plasma cell dyscrasias, or rare hematologic disorders. Familiarity with eCTD publishing, regulatory information management systems, and modern regulatory operations tooling. Experience contributing to or leading regulatory components of due diligence, partnering, or capital-raising activities. Salary: $228,000 - $315,000 a year In addition to a competitive base salary ranging from $285,000 to $315,000, we offer stock options, and a target bonus. Protego also provides a comprehensive benefits package for our employees and their families, which includes medical, dental, vision, and supplemental disability insurance. Please note that the salary range is a guideline, and individual total compensation will vary based on factors such as qualifications, skill level, competencies, and internal equity. Job Type: Full-time Incentive stock option plan 401k plan with employer contribution Dental and vision insurance HSA, FSA, and supplemental insurance plans (life, disability, accident, critical illness) Paid Time Off Company Paid Holidays Schedule Monday to Friday Work Authorization United States (Required) Additional Compensation Annual targeted bonus % Work Location: Hybrid preferred in San Diego office with ability to travel up to 25% for meetings or site visits as required. Equal Opportunity Employer Protego Biopharma is an equal opportunity employer that is committed to providing a work environment free of harassment and discrimination based upon a protected category, as well as an environment free from retaliation for protected activity. We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses. These tools assist our recruitment team but do not replace human judgment. 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