Senior Principal Scientist, Applied AI & Agentic Systems for Small-Molecule Drug Discovery

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

Benefits offered by this job

Medical benefits

Dental benefits

Vision benefits

Paid time off

Educational assistance

Commuting subsidy

401(k)

Job summary

Vertex Pharmaceuticals Inc. is seeking a leader to drive scientific transformation through applied AI and agentic systems in small-molecule drug discovery.

You will collaborate with project teams to deploy AI co-scientists for SAR analysis, molecular design, and lead optimization, leveraging computational chemistry and AI methods. The role emphasizes establishing evaluation benchmarks, responsible AI governance, and measurable impact on discovery productivity, with a Boston-based hybrid work

Qualifications

• PhD in a relevant scientific discipline with leadership in computational methods.
• 8+ years applying computational chemistry/cheminformatics to drug discovery.
• Experience translating scientific opportunities into scalable computational capabilities.
• Strong understanding of AI methods and governance in research environments.

Responsibilities

• Lead AI-enabled scientific transformation across small-molecule drug discovery.
• Partner with teams to deploy AI co-scientists for SAR analysis and design.
• Define evaluation frameworks and benchmarks for AI tools.
• Drive adoption and measurable impact while ensuring responsible AI standards.
• Act as a thought leader for AI-enabled scientific innovation.

Skills

Computational chemistry

Cheminformatics

Machine learning

AI governance

Cross-functional collaboration

Education

PhD in Computational Chemistry, Chemistry, Computer Science, Data Science, Engineering or related

Job description

Key Duties and Responsibilities

• Lead Scientific Transformation Through Applied AI and Agentic Systems Drive the strategic application of AI and agentic systems across small-molecule drug discovery, while identifying opportunities to extend broadly applicable capabilities to protein therapeutics and other modalities.
• Partner with project teams and scientific leaders to develop and deploy AI co-scientists that support knowledge synthesis, SAR analysis, scientific question answering, experiment planning, virtual screening, molecular design, and lead optimization, leveraging established computational chemistry and cheminformatics approaches alongside modern AI methods.
• Define scientific evaluation frameworks, benchmarks, and validation strategies to ensure AI systems generate reliable, evidence-based, and actionable scientific insights.
• Establish success metrics and drive measurable impact through increased scientific productivity, faster information synthesis, improved decision quality, and more efficient DMTA cycles.
• Serve as a thought leader and ambassador for AI-enabled scientific innovation across Discovery Research.

Location: Boston based, hybrid position requiring 3 days per week onsite.

Lead Platform Strategy, Adoption, and Responsible AI Operations

• Serve as the scientific bridge between Drug Discovery, Data & Methods, and Digital Technology & Engineering, translating scientific needs into scalable AI and agentic capabilities.
• Provide scientific product leadership for AI-enabled workflows, ensuring solutions are aligned with discovery priorities and integrated into day-to-day scientific practice.
• Define operational guardrails governing model usage, data access, computational resources, cost management, approval workflows, monitoring, and intervention mechanisms.
• Drive adoption through scientist engagement, education, change leadership, and continuous improvement while ensuring compliance with Vertex data governance, cybersecurity, and responsible AI standards.

Knowledge and Skills

• Deep understanding of small-molecule drug discovery and the DMTA cycle, with firsthand experience applying computational chemistry and cheminformatics approaches to guide molecular design, lead optimization, and project decision-making.
• Expertise in one or more of the following areas: computational chemistry, cheminformatics, molecular design, machine learning, scientific data science, or computational drug discovery with a proven ability to apply these methods to discover, optimise, and advance drug candidates.
• Strong understanding of modern AI technologies, including large language models, agentic systems, retrieval-augmented workflows, and AI-assisted scientific applications.
• Demonstrated ability to define scientific evaluation frameworks, benchmarks, and validation strategies for AI-enabled research tools.
• Deep knowledge of scientific rigor, data provenance, reproducibility, AI governance, and responsible AI practices in research environments.
• Ability to balance scientific impact, user experience, computational cost, and operational complexity when designing and deploying AI-enabled workflows.
• Strong product-thinking skills, including the ability to translate scientific challenges into scalable capabilities that deliver measurable value.
• Understanding of the scientific workflows and data modalities associated with protein therapeutics, biologics, or other emerging therapeutic modalities is strongly preferred.
• Excellent communication, collaboration, and stakeholder-management skills, with the ability to influence scientists, engineers, data scientists, and senior leaders across a matrixed organization.

Education and Experience

• Ph.D. in Computational Chemistry, Chemistry, Computer Science, Data Science, Engineering or a related scientific discipline.
• Recognised scientific leader with 8+ years of experience applying computational chemistry, cheminformatics, and related computational approaches to advance small-molecule drug discovery programmes and deliver candidate molecules.
• 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 organisations.
• Proven ability to lead complex cross-functional initiatives and influence scientific strategy without direct authority.
• Track record of driving adoption of new computational technologies and leading scientific or organisational transformation.
• Experience applying computational, data science or AI approaches to protein therapeutics, biologics, or other therapeutic modalities is strongly preferred.

Pay Range

Pay Range: $168,000 - $252,000

Benefits

• 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 programmes including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more.

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; or select 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, colour, 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].

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 recognised 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.

Why Join Us

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.