Process Chemistry Principal Scientist

Vertex Pharmaceuticals; Boston (MA); On-site; USD 138,000 - 207,000; Full time

Benefits offered by this job

Annual bonus

Equity awards

On-site work

Comprehensive benefits

Job summary

Vertex Pharmaceuticals in Boston seeking a highly experienced Principal Scientist to lead preparative chromatography and kilo-lab scale purification. The role spans R&D and cGMP operations, guiding method development, scale-up, and lab infrastructure for drug substance purification.

You will mentor staff, collaborate with Process Chemistry, Analytical Development and Quality, and ensure compliance with Vertex quality systems while advancing pipeline programs.

Qualifications

• Expert-level proficiency in preparative chromatography across scales and modes.
• Track record in leading cross-functional separations projects and lab initiatives.
• Experience in cGMP pharmaceutical environments and kilo-lab operations.

Responsibilities

• Lead development and scale-up of preparative purification methods (HPLC/SFC).
• Execute complex purification campaigns and troubleshoot separations.
• Build and maintain kilo-lab synthesis and purification infrastructure.
• Mentor scientific staff and author GMP documentation.

Skills

Preparative chromatography

HPLC

SFC

IP-RP_HPLC

AEX/CEX

SEC

Leadership

Cross-functional collaboration

Education

PhD in Analytical/Organic/Medicinal Chemistry or related

MS/BS with extensive industry experience

Tools

Empower

OpenLab

Job description

Job DescriptionGeneral 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 profileExecute & 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 solutionsEstablish & 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 capabilityPerform 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 yieldSupport 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 decisionsBuild 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 establishmentMentor & 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 operationsAuthor & 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 systemsLead 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 groupsEnsure 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 expertKnowledge 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 leadershipExperience mentoring and developing junior scientists and technical staff, fostering growth in separations techniques and kilo-lab operationsDeep 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 protocolsDemonstrated commitment to laboratory safety, environmental health standards , and maintaining a culture of quality and compliance across all operationsAbility 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 decisionsEducation 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 experienceAt Vertex, we embrace continuous learning and encourage employees to stay informed on advances in AI, technology, automation, and industry trends. We seek talent who bring an external perspective, demonstrate curiosity and sound judgment, and thoughtfully adopt new capabilities that improve decision-making, drive innovation, increase efficiency, and help deliver better outcomes for patients.Pay Range:$138,000 - $207,000Disclosure Statement:The range provided is based on what we believe is a reasonable estimate for the base salary pay range for this job at the time of posting. This role is eligible for an annual bonus and annual equity awards. Some roles may also be eligible for overtime pay, in accordance with federal and state requirements. Actual base salary pay will be based on a number of factors, including skills, competencies, experience, and other job-related factors permitted by law.At Vertex, our Total Rewards offerings also include inclusive market-leading benefits to meet our employees wherever they are in their career, financial, family and wellbeing journey while providing flexibility and resources to support their growth and aspirations. From medical, dental and vision benefits to generous paid time off (including a week-long company shutdown in the Summer and the Winter), educational assistance programs including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more.Flex Designation:On-Site DesignatedFlex Eligibility Status:In this On-Site designated role, you will work five days per week on-site with ad hoc flexibility.Note: The Flex status for this position is subject to Vertex’s Policy on Flex @ Vertex Program and may be changed at any time.#LI-OnsiteCompany InformationVertex is a global biotechnology company that invests in scientific innovation.Vertex is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E-Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law.Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at [e-mail]