Senior Process Engineer, MSAT, Drug Substance

Amylyx Pharmaceuticals

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

Posted 11/6/2026full-timeRemote • Massachusetts • United StatesSenior💰 $156,000 - $176,000 per yearWebsite

Core Competencies

Role fit

Core Competencies

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Demonstrates expertise in process engineering for drug substance manufacturing, with a strong focus on compliance with cGMPs and global regulatory requirements. Capable of leading technology transfer, process validation, and continuous improvement initiatives while effectively communicating complex technical information.

Highest-signal resume keywords

Process ValidationCGMP ComplianceTechnology TransferRoot Cause AnalysisRegulatory Submissions

ATS Keywords

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Applicant Tracking System Keywords

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Hard Skills

Process EngineeringChromatography PurificationUltrafiltrationDiafiltrationLyophilizationStatistical Process ControlQuality by DesignDesign of ExperimentsCAPA DevelopmentRisk Assessment

Soft Skills

Excellent Communication SkillsLeadershipInfluencing Cross-Functional DecisionsAnalytical ThinkingCollaboration

Tools & Technologies

MATLABJMPData RepositoriesDashboardsKPI Assessment

Industry Keywords

Peptide Drug Substance ManufacturingBiologic ManufacturingRegulatory FilingsChange ControlProcess Capability

About the role

Key responsibilities & impact

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 subject matter expert during manufacturing operations, providing onsite support when required
Lead investigations, perform root cause analysis, and develop scientifically sound CAPAs
Author technical risk assessments and change controls for manufacturing changes, investigations, and regulatory filings
Ensure compliance with cGMPs, global regulatory requirements, and internal quality systems
Review and provide technical input into master batch records, campaign readiness plans, process descriptions, and manufacturing documentation
Lead drug substance technology transfer between clinical, validation, and commercial manufacturing sites
Define critical process parameters, critical quality attributes, and in-process controls for peptide drug substance operations
Develop and execute process validation strategies, including PPQ planning, statistical sampling plans, and acceptance criteria
Provide technical authorship and review for IND, BLA, NDA, and MAA submissions, validation reports, and regulatory responses
Support drug substance introductions and commercial launches by ensuring processes are validated, scalable, robust, and inspection ready
Lead continued process verification and routine data trending
Develop and maintain data repositories, dashboards, and KPIs to assess process capability, performance, and trends
Identify process drift, yield loss, impurity shifts, raw material variability, and scale-dependent risks; drive corrective or preventive actions
Prepare and present quarterly CPV summaries and technical assessments for management reviews
Execute continuous improvement initiatives focused on process robustness, impurity control, yield, cycle time, capacity, and operational efficiency
Apply Quality by Design, Design of Experiments, statistical process control, and risk-based decision making
Collaborate with CDMOs to implement best practices, new technologies, and process enhancements

Requirements

What you’ll need

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 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: Experience with liquid-phase, hybrid, tag-assisted synthesis, or green chemistry approaches for peptide manufacturing
Preferred: Experience with modeling, statistical analysis, or process optimization tools such as MATLAB or JMP
Preferred: Experience supporting regulatory submissions, health authority questions, inspections, and commercial launch readiness
Must have access to a remote work setting with privacy, reliable internet access, phone, and video conferencing capability
Applicants must reside and/or work in the United States; applicants from Alaska and Hawaii are not currently being considered

Benefits

Comp & perks

Annual performance-based bonuses for eligible employees
Equity awards for eligible employees
Comprehensive benefits package supporting health, well-being, and financial security
Remote work opportunities within the United States
Company-related events
Equal opportunity employment
Accommodations available during the selection process