Senior Process Engineer, MSAT, Drug Substance

Amylyx Pharmaceuticals•Cambridge, MA

3d•$156,000 - $176,000•Remote

About The Position

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.

Requirements

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%.

Nice To Haves

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.

Responsibilities

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.
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.
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.
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.