Senior Process Engineer, MSAT, Drug Substance

Amylyx has an audacious mission to usher in a new era for treating diseases with high unmet needs. Where others see challenges, we see opportunities that we pursue with urgency, rigorous science, and unwavering commitment to the communities we serve. We are a clinical-stage company currently focused on post-bariatric hypoglycemia (PBH), Wolfram syndrome, and amyotrophic lateral sclerosis (ALS).

Our mission is powered by our people. Our core values – be audacious, be curious, be authentic, be engaged, and be accountable – creating a culture of caring. Amylyx has assembled an experienced team ready to take action because the communities we serve have no time to wait. If you share our passion and are determined to tackle some of medicine’s toughest problems, we encourage you to read the opportunity below and apply.

The Opportunity

Amylyx is seeking a Senior Process Engineer, MSAT, Drug Substance to provide technical and GMP leadership for late-stage clinical and commercial peptide drug substance manufacturing performed at external contract development and manufacturing organizations (CDMOs). Reporting to the Director, Manufacturing Sciences and Technology, this role will serve as process owner and technical subject matter expert for avexitide drug substance and partner across Quality, Quality Control, CMC, and External Manufacturing. The Senior Process Engineer will lead technology transfer, process validation, continued process verification, investigations, change control, and process lifecycle management to support reliable, compliant, and efficient manufacturing.

Responsibilities

Manufacturing Support:

Provide technical leadership and day-to-day process engineering support for clinical and commercial drug substance manufacturing at external CDMOs.

Serve as the process engineering SME during manufacturing operations, providing onsite support when required.

Lead investigations, perform rigorous root cause analysis and develop scientifically sound CAPAs, ensuring alignment with regulatory expectations and industry best practices.

Assess and author technical risk assessments and change controls to support manufacturing changes, investigations, and regulatory filings.

Ensure strict compliance with cGMPs, global regulatory requirements, and internal quality systems for drug substance manufacturing.

Review and provide technical input into master batch records, campaign readiness plans, process descriptions, and manufacturing documentation to ensure process requirements are accurately translated into GMP execution.

Process Validation:

Lead drug substance technology transfer activities between clinical, validation, and commercial manufacturing sites.

Define critical process parameters (CPPs), critical quality attributes (CQAs), and in‑process controls for peptide drug substance unit operations.

Develop and execute process validation strategies, including PPQ planning, statistical sampling plans, and acceptance criteria aligned with regulatory guidance.

Provide technical authorship and review for regulatory submissions (IND, BLA, NDA, MAA), validation reports, and responses to regulatory agency questions.

Support new drug substance introductions and commercial launches by ensuring peptide manufacturing processes are validated, scalable, robust, and inspection ready.

Data Analysis & Continued Process Verification:

Lead continued process verification (CPV) and routine data trending for manufacturing unit operations, in-process controls, and critical process parameters.

Develop and maintain data repositories, dashboards, and meaningful KPIs to assess process capability, performance, and trends.

Identify early signals of process drift, yield loss, impurity shifts, raw material variability, or scale-dependent performance risks and proactively drive corrective or preventive actions.

Prepare and present quarterly CPV summaries and technical assessments for internal management reviews.

Continuous Improvement:

Identify and execute continuous improvement initiatives focused on process robustness, impurity control, yield, cycle time, capacity, and operational efficiency.

Apply Quality by Design (QbD), Design of Experiments (DoE), statistical process control (SPC), and risk-based decision making to optimize drug substance manufacturing processes.

Collaborate with CDMOs to implement best practices, new technologies, or process enhancements where appropriate.

Required Qualifications

Bachelor’s degree in chemical engineering or a related field with 8 or more years of relevant experience, or a master’s degree with 5 or more years of relevant experience.

Experience supporting late-phase or commercial peptide or biologic drug substance manufacturing, including downstream operations such as chromatography purification, ultrafiltration or diafiltration, and lyophilization.

Comprehensive knowledge of cGMP principles, quality systems, global regulatory expectations, and process, equipment, and facility validation requirements.

Demonstrated experience with technology transfer, process validation, continued process verification, manufacturing investigations, CAPAs, risk assessments, and change control.

Ability to analyze complex manufacturing data, identify subtle process trends, and translate findings into practical, scientifically sound actions.

Demonstrated ability to lead technical discussions with external partners and influence cross-functional decisions without direct authority.

Excellent written and verbal communication skills, with the ability to communicate complex process risks to technical and non-technical stakeholders.

Ability to travel domestically and internationally to CDMO sites up to 20%.

Preferred Requirements

Experience with liquid-phase, hybrid, tag-assisted synthesis, or green chemistry approaches for peptide manufacturing.

Experience with modeling, statistical analysis, or process optimization tools such as MATLAB or JMP.

Experience supporting regulatory submissions, health authority questions, inspections, and commercial launch readiness.

Work Location and Conditions

At Amylyx, we proudly support remote work opportunities within the United States. However, due to business considerations related to health insurance coverage and state tax regulations, we are unable to hire employees who reside and/or work in certain states. Currently, we are not considering applicants from Alaska and Hawaii.

You will be expected to travel to our corporate location in Cambridge, MA several times a year and attend other company-related events as necessary and requested.

You must have access to work in setting which enables meeting all requirements of the role (including privacy, reliable internet access, phone, ability to video conference, etc.) at your remote location.

Compensation

The pay range posted below represents our good faith estimate of compensation for this role, based on market data and internal benchmarks. The final offer may vary depending on a candidate’s experience, skills, and qualifications, as well as considerations of internal equity.

Base salary is one component of Amylyx’s total rewards package. In addition to competitive base pay, eligible employees may receive annual performance-based bonuses and equity awards, providing an opportunity to share in the company’s long-term success. Amylyx also offers a comprehensive benefits package designed to support the health, well-being, and financial security of our employees.

Estimated Pay Range$156,000—$176,000 USD

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Amylyx Pharmaceuticals is an Equal Opportunity Employer that does not discriminate on the basis of actual or perceived race, color, creed, religion, national origin, ancestry, citizenship status, age, sex or gender (including pregnancy, childbirth, pregnancy-related conditions, and lactation), gender identity or expression (including transgender status), sexual orientation, marital status, military service and veteran status, physical or mental disability, genetic information, or any other characteristic protected by applicable federal, state, or local laws and ordinances. Amylyx’s management team is dedicated to this policy with respect to recruitment, hiring, placement, promotion, transfer, training, compensation, benefits, employee activities, access to facilities and programs, and general treatment during employment. Accommodations are available for candidates who require them in our selection process. If you need an accommodation, please let your Amylyx Talent Acquisition contact know.

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.