Principal Scientist R&D & cGMP Preparative Chromatography

Job Description General Summary: 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, environmental health standards , and maintaining a culture of quality and compliance across all operations Ability to flex into hands-on synthetic organic chemistry at kilogram scale, including jacketed reactor operations, large-scale workups, and the ability to interpret complex analytical data (HPLC, LC-MS, NMR, Karl Fischer) to drive purification and synthetic decisions Education and Experience: Ph.D. in Analytical Chemistry, Organic Chemistry, Medicinal Chemistry, Chemical Engineering, or a closely related discipline preferred; M.S. or B.S. with extensive relevant industry experience will be considered. Bachelor’s degree and 10+ years, Master’s degree and 7+ years, or PhD and 4+ years of hands-on industry experience in R&D and cGMP pharmaceutical analytical and preparative separations, drug substance development manufacturing or the equivalent combination of education and experience At Vertex, we embrace continuous learning and enco