Process Chemistry Principal Scientist

Vertex Pharmaceuticals Inc (US); United States; On-site; USD 138,000 - 207,000; Full time

Job summary

Vertex Pharmaceuticals is seeking a highly experienced Principal Scientist for the Vertex Manufacturing Center's kilo-lab, focusing on analytical and preparative chromatography for drug substance development in both R&D and cGMP settings.

The role requires leading method development for HPLC/SFC, scale-up campaigns from semi-prep to kilogram scale, and collaboration with Process Chemistry, Analytical Development, Quality, and Manufacturing to drive scalable routes and deliver high-quality drug

Qualifications

• Ph.D. in Analytical Chemistry, Organic Chemistry, Medicinal Chemistry, Chemical Engineering, or 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

Responsibilities

• Lead preparative chromatography method development and scale-up from semi-preparative to kilogram scales for R&D and cGMP.
• Execute complex purification campaigns, troubleshoot separations, and develop solutions.
• Build and maintain lab infrastructure, procure equipment, qualify systems, and influence lab strategy.
• Perform kilo-lab scale synthesis with safety, quality, and yield accountability.
• Collaborate with Process Chemistry and Analytical Development to implement scalable routes and interpret analytical data (NMR, HPLC, MS).
• Define roadmap for kilogram oligonucleotide purification platforms and oversee equipment qualification and SOPs.
• Mentor and train junior scientists and technicians in preparative chromatography and kilo-lab operations.
• Author and review GMP documentation, SOPs, master batch records, validation protocols, and purification reports.
• Lead cross-functional technical initiatives as SME for preparative purification and drug substance chemistry.
• Ensure cGMP compliance, quality, safety, and audit readiness.

Skills

Preparative chromatography

HPLC

SFC

IP-RP HPLC

AEX/CEX

SEC

Scale-up purification

cGMP operations

Analytical development

Mentoring staff

Education

PhD in Analytical/Organic/Medicinal Chemistry or Chemical Engineering

MS/BS with extensive industry experience

Tools

Empower

OpenLab

Mass-directed purification

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, 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, KarlFischer) 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 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:

Pay Range: $138,000 - $207,000 Disclosure 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:

Flex Designation: On‑Site Designated Flex 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‑Onsite

Company Information

Vertex 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. Help Us Achieve Our Mission Vertex is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases and conditions. The company has approved therapies for cystic fibrosis, sickle cell disease, transfusion‑dependent beta thalassemia, acute pain and acromegaly, and it continues to advance clinical and research programs in these areas. Vertex also has a robust clinical pipeline of investigational therapies across a range of modalities in other serious diseases where it has deep insight into causal human biology, including IgA nephropathy, neuropathic pain, APOL1‑mediated kidney disease, primary membranous nephropathy, congenital adrenal hyperplasia, ACTH‑dependent Cushing’s syndrome, autosomal dominant polycystic kidney disease, type1 diabetes, generalized myasthenia gravis, and myotonic dystrophy type 1. Vertex was founded in 1989 and has its global headquarters in Boston, with international headquarters in London. Additionally, the company has research and development sites and commercial offices in North America, Europe, Australia, Latin America and the Middle East. Vertex is consistently recognized as one of the industry's top places to work, including 16 consecutive years on Science magazine’s Top Employers list and one of Fortune’s 100 Best Companies to Work For. For company updates and to learn more about Vertex's history of innovation, visit www.vrtx.com or follow us on LinkedIn, Facebook, Instagram, YouTube, and X We believe our culture is one of Vertex’s greatest strengths and a key enabler of our ability to deliver transformative medicines for patients who need them. Rooted in innovation, purpose and collaboration, our culture empowers people to take smart risks, challenge conventional thinking and do their best work. The diversity of our people is central to that culture. By bringing together individuals with different backgrounds, experiences and perspectives, we foster an environment where new ideas thrive, better decisions are made and breakthrough innovation is possible. We are committed to creating a workplace where everyone feels valued, included and connected to our shared mission, because we know that our unique culture and the collective strength of our people are what set Vertex apart.