Senior Principal Scientist, Agentic Systems Development for Drug Discovery

Vertex Pharmaceuticals Inc (US); United States; Hybrid; USD 168,000 - 252,000; Full time

Benefits offered by this job

Annual bonus

Equity awards

Job summary

Vertex Pharmaceuticals Inc is seeking a Senior Principal Scientist to lead development and deployment of agentic AI for drug discovery, with emphasis on small molecules and cheminformatics. This Boston-based, hybrid role requires 3 days on-site weekly.

You will collaborate across computational scientists and software engineers to deliver production-grade AI workflows, apply CI/CD and DevOps practices, and drive AI-enabled decision-making across discovery programs.

Qualifications

• PhD in Computational Chemistry, Cheminformatics, or related field.
• 8+ years in scientific software development for drug discovery.
• Experience deploying AI-enabled scientific products, platforms, or applications.
• Demonstrated success translating scientific opportunities into scalable AI capabilities with measurable impact.
• Significant cross-disciplinary experience across discovery, computational sciences, data science, and engineering.

Responsibilities

• Translate scientific requirements into agentic AI solutions that autonomously reason, plan, and execute complex tasks.
• Build, test, and deploy AI-enabled solutions that support drug discovery across small molecules and proteins.
• Collaborate with computational scientists, software engineers, and cross-functional project teams to deliver scalable AI solutions.
• Apply software engineering, DevOps, and compliance best practices to deliver production-grade AI systems.
• Design and implement testing, evaluation, and validation strategies for agentic AI systems.
• Contribute to innovation efforts that realize value from Agentic AI and Generative AI technologies.
• Stay current with emerging agentic AI patterns and prototype new capabilities to evaluate their scientific impact.

Skills

Agentic AI

Python

CI/CD

DevOps

Cheminformatics

Small molecules

Machine learning

Communication

Team collaboration

Software development

Education

PhD in Computational Chemistry

Tools

CI/CD pipelines

Job description

Job Description Vertex is seeking an accomplished Senior Principal Scientist with proven record of developing, testing and deploying scientific computational methods and agentic AI systems for drug discovery. In this role, you will work across modalities with emphasis on small molecules to develop, test, and deploy AI-enabled solutions that enhance scientific workflows, improve decision-making, and increase productivity. As a scientific developer and trusted scientific computational methods and cheminformatics expert, you will establish AI testing and evaluations strategies and drive the development of high performant, AI-enabled scientific workflows. This is a highly collaborative position at the intersection of computational sciences, research teams, and Digital Technology & Engineering. This is a Boston based, hybrid position requiring 3 days/week onsite.

Key Duties and Responsibilities

• Translate scientific requirements into agentic AI solutions that can autonomously reason, plan, and execute complex tasks
• Build, test, and deploy AI-enabled solutions that support drug discovery across small molecule and protein therapeutics
• Collaborate with computational scientists, software engineers, and cross-functional project teams to deliver scalable AI solutions
• Apply software engineering, DevOps, and compliance best practices to deliver production-grade AI systems
• Design and implement testing, evaluation, and validation strategies for agentic AI systems
• Contribute to innovation efforts that help research programs realize value from Agentic AI and Generative AI technologies.
• Stay current with emerging agentic AI patterns and prototype new capabilities to evaluate their scientific impact.

Knowledge and Skills

• Deep understanding of drug discovery, with the ability to bridge the gap between scientific requirements and production-ready AI solutions
• Expert knowledge of small molecule scientific computational methods and cheminformatics
• Working knowledge of building AI agents including tools, orchestration and multi-step reasoning
• Strong experience with scientific software development; well versed in CI/CD and DevOps practices
• Strong Python skills and solid machine learning/AI foundations - able to write clean, production-grade code with a firm grasp of system design principles
• Expertise in one or more of the following areas: cheminformatics, machine learning, computational drug discovery, scientific data science
• Strong understanding of modern AI technologies, including large language models, agentic systems, retrieval-augmented workflows, and AI-assisted scientific applications
• Excellent communication skills, collaboration, and stakeholder-management skills; can explain technical trade-offs to non-technical stakeholders.

Education and Experience

• Ph.D. in Computational Chemistry, Cheminformatics, or a related scientific discipline
• More than 8 years of experience in scientific software development and application to drug discovery programs
• Hands-on experience developing, deploying, and managing AI-enabled scientific products, platforms, or applications
• Demonstrated success translating scientific opportunities into scalable computational, data science, software, or AI capabilities that deliver measurable scientific and business impact
• Significant experience working across discovery research, computational sciences, data science, and engineering organizations
• Experience applying AI, machine learning, or advanced computational methods to real-world drug discovery challenges

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: $168,000 - $252,000 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: Hybrid-Eligible Or On-Site Eligible Flex Eligibility Status: In this Hybrid-Eligible role, you can choose to be designated as:

1. Hybrid: work remotely up to two days per week;
2. On-Site: 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.

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.