Medicinal Chemistry Senior Principal Research Scientist

Vertex Pharmaceuticals Inc (US); San Diego (CA); On-site; USD 164,000 - 247,000; Full time

Job summary

Vertex Pharmaceuticals is seeking a Senior Principal Research Scientist in Medicinal Chemistry to provide scientific leadership across discovery programs. You will design and optimize small-molecule therapeutics, guiding synthesis and leading cross-functional teams to drive progress from discovery through candidate selection.

The role emphasizes strategic thinking, SAR interpretation, and collaboration with biology, DMPK, toxicology, and pharma sciences.

Qualifications

• Ph.D. in Chemistry or related scientific discipline with 6+ years of relevant postdoctoral industry experience; Master’s degree with 9+ years of relevant industry experience; or Bachelor’s degree with 11+ years of relevant industry experience.
• Significant experience in medicinal chemistry and small-molecule drug discovery.
• Demonstrated success advancing discovery programs through candidate selection.
• Experience leading cross-functional and multidisciplinary teams including in matrixed settings.
• Strong communication, strategic thinking, decision-making, prioritization, and problem-solving skills.

Responsibilities

• Lead medicinal chemistry strategy for small-molecule discovery programs aligned with portfolio and project objectives.
• Design, prioritize, and guide synthesis of novel compounds to optimize potency, selectivity, pharmacokinetics, and developability.
• Interpret and integrate SAR, structural biology, DMPK, pharmacology, and safety data to drive compound design and progression.
• Partner closely with biology, DMPK, toxicology, and pharmaceutical sciences to advance program goals.
• Provide technical and strategic leadership to internal and external chemistry resources.
• Provide scientific leadership, mentorship, and development support to chemistry team members.
• Communicate program strategy, data, risks, and recommendations to senior leadership and governance teams.
• Support intellectual property strategy in partnership with internal stakeholders.

Skills

Medicinal chemistry

Organic synthesis

Small-molecule drug discovery

Lead optimization

SAR analysis

Compound design

Candidate selection

DMPK/ADME collaboration

Drug property optimization

Patent support

Education

Ph.D. in Chemistry or related field

Master’s degree with 9+ years of experience

Bachelor’s degree with 11+ years of experience

Job description

Job Description Vertex is seeking a Senior Principal Research Scientist, Medicinal Chemistry to provide scientific leadership in the design and optimization of small-molecule therapeutics across discovery programs. Leading from the lab, this role will play a critical part in advancing high-quality drug candidates from early discovery through candidate selection, while partnering across multidisciplinary teams to solve complex scientific challenges. The ideal candidate is an accomplished medicinal chemist with deep expertise in small-molecule drug discovery, a strong record of scientific innovation, and demonstrated success in a fast-paced and matrixed research environment. This is an on-site role with approximately 75% of time being spent in the lab.

Key Responsibilities

• Lead medicinal chemistry strategy for small-molecule discovery programs aligned with portfolio and project objectives.
• Design, prioritize, and guide synthesis of novel compounds to optimize potency, selectivity, pharmacokinetics, and developability.
• Interpret and integrate SAR, structural biology, DMPK, pharmacology, and safety data to drive compound design and progression.
• Partner closely with biology, DMPK, toxicology, and pharmaceutical sciences to advance program goals.
• Provide technical and strategic leadership to internal and external chemistry resources.
• Provide scientific leadership, mentorship, and development support to chemistry team members.
• Communicate program strategy, data, risks, and recommendations to senior leadership and governance teams.
• Support intellectual property strategy in partnership with internal stakeholders.

Knowledge and Skills

• Medicinal chemistry
• Organic synthesis
• Small-molecule drug discovery
• Lead optimization
• SAR analysis
• Compound design
• Candidate selection
• DMPK/ADME collaboration
• Drug property optimization
• Patent support

Education and Experience

• Ph.D. in Chemistry or related scientific discipline with 6+ years of relevant postdoctoral industry experience; Master’s degree with 9+ years of relevant industry experience; or Bachelor’s degree with 11+ years of relevant industry experience.
• Significant experience in medicinal chemistry and small-molecule drug discovery.
• Demonstrated success advancing discovery programs through candidate selection.
• Experience leading cross-functional and multidisciplinary teams including in matrixed settings.
• Strong communication, strategic thinking, decision-making, prioritization, and problem-solving skills.

#LI-KM1 #LI-Onsite

Pay Range

$164,400 - $246,600 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

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.

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. 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]

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, type 1 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.