Process Chemistry Principal Scientist

Vertex Pharmaceuticals; Boston (MA); On-site; USD 180,000 - 240,000; Full time

Job summary

Vertex Pharmaceuticals seeks a highly experienced Principal Scientist for the Vertex Manufacturing Center (VMC) Kilo Lab. You will lead preparative chromatography method development, scale-up, and cross-functional collaboration across R&D and cGMP environments.

This role requires hands-on leadership, strong chromatography expertise (HPLC, SFC, IP-RP, AEX/CEX, SEC), and the ability to drive complex purification campaigns from lab to kilo-scale while ensuring safety, quality, and reproducibility.

Qualifications

• Extensive experience developing and scaling preparative chromatography methods for drug substances.
• Proven ability to lead cross-functional purification campaigns in cGMP environments.
• Strong documentation, method transfer, and tech leadership skills.

Responsibilities

• Lead development and scale-up of preparative chromatography from semi-preparative to kilogram scale.
• Troubleshoot complex purification campaigns and optimize impurity profiles.
• Build and maintain large-scale chromatography platforms and qualify systems.
• Perform kilo-lab synthesis with scale-up into multi-step routes and ensure safety and yield.
• Collaborate with Process Chemistry, Analytical Development, Quality, and Manufacturing.
• Mentor junior scientists and author GMP documentation and SOPs.

Skills

Preparative chromatography

HPLC

SFC

IP-RP

AEX

CEX

SEC

Chromatography data systems

Leadership

Cross-functional collaboration

Education

PhD or MSc in a relevant field

Tools

Empower

OpenLab

Job description

Vertex Pharmaceuticals is seeking a highly experienced and motivated Principal Scientist to join the Vertex Manufacturing Center (VMC) Kilo Lab in a dual-capability role that is central to our drug substance development mission. This is an exceptional opportunity for a seasoned pharmaceutical scientist with deep expertise in analytical and preparative chromatographic purification in both an R&D and cGMP environment- including large-scale preparative HPLC, supercritical fluid chromatography (SFC), Ion-pair reversed phase high-performance liquid chromatography (IP-RP_HPLC), ion exchange chromatography (AEX/CEX), and size exclusion chromatography (SEC). This individual will play a pivotal role in jumpstarting Vertex's emerging kilo-scale cGMP purification capabilities and laboratory, contributing also to new therapeutic modalities with significant pipeline impact.

Key Duties and Responsibilities

• Lead Preparative Chromatography Method Development Spearhead the development, optimization, and scale-up of preparative HPLC and SFC purification methods across all scales - from semi-preparative to kilogram for both R&D and cGMP- selecting appropriate chromatographic modes (RP, NP, IEX, SEC) based on compound class and impurity profile
• Execute & Troubleshoot Complex Purification Campaigns Lead hands-on execution of mass-directed and preparative purification campaigns for complex small molecule drug substances, troubleshooting challenging separations and developing creative, scientifically sound solutions
• Establish & Maintain Lab Infrastructure: Drive equipment procurement, column packing, system qualification, and ongoing maintenance of large-scale chromatography platforms; influence technology selection and lab infrastructure investments to build a world-class separations capability
• Perform Kilo-Lab Scale Synthesis: Ability to flex into multi-step synthesis of drug substance intermediates and APIs at gram-to-kilogram scale, including reactions in jacketed vessels and large-scale reactor systems, with full accountability for safety, quality, and yield
• Support Scale-Up & Process Chemistry Collaboration: Partner with Process Chemistry , Analytical DevelopmentD and project teams to implement and adapt synthetic routes for kilo-lab operations, performing workups, crystallizations, filtrations, and drying at scale, and interpreting analytical data (NMR, HPLC, MS) to drive process decisions
• Build Peptide and Oligonucleotide Purification Capability: Define the strategic roadmap and lead the implementation of kilogram oligonucleotide synthesis (solid-phase phosphoramidite chemistry) and purification platforms (IP-RP HPLC, AEX/CEX, ultrafiltration/diafiltration), including equipment procurement, qualification, and SOP establishment
• Mentor & Develop Scientific Staff: Provide hands-on mentorship, technical coaching, and structured training to junior scientists, associates, and technicians - equipping them to independently master preparative chromatography, separations techniques, and kilo-lab operations
• Author & Own GMP Documentation: Author, review, and approve SOPs, master batch records, validation protocols, purification reports, and technical documents in full compliance with cGMP standards and Vertex quality systems
• Lead Cross-Functional Technical Initiatives: Serve as the organizational SME for preparative purification and drug substance chemistry; lead cross-functional project teams and act as primary technical liaison with Analytical Development, Process Chemistry, Quality, and Manufacturing groups
• Ensure GMP Compliance, Quality & Safety: Ensure all lab operations adhere strictly to cGMP regulations, EHS standards, and Vertex quality requirements; maintain meticulous documentation (ELN, batch records, deviations, change controls) and support internal/external audits as a subject matter expert

Knowledge and Skills

• Expert-level proficiency in preparative chromatography (HPLC, SFC, IP-RP, AEX, CEX SMB, and SEC) across all scales, encompassing method development, column selection, mobile phase optimization, mass-directed purification systems, and chromatography data systems (e.g., Empower, OpenLab)
• Demonstrated track record of technical leadership and cross-functional collaboration , with the ability to influence stakeholders, lead project teams, and drive scientific decisions without direct authority.
• Strong written and verbal communication skills, with proven ability to present complex technical findings to diverse audiences ranging from bench scientists to senior leadership
• Experience mentoring and developing junior scientists and technical staff, fostering growth in separations techniques and kilo-lab operations
• Deep working knowledge of cGMP regulations, documentation standards, and quality systems as applied to drug substance manufacturing, including authoring and reviewing batch records, SOPs, deviation reports, and validation protocols
• Demonstrated commitment to laboratory safety,