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

Vertex Pharmaceuticals Incorporated; Boston (MA); Hybrid; USD 168,000 - 252,000; Full time

Benefits offered by this job

Annual bonus

Annual equity awards

Comprehensive benefits

Job summary

Vertex Pharmaceuticals Incorporated is seeking a scientific leader to accelerate AI-driven drug discovery, blending computational chemistry, cheminformatics and modern AI to transform design-make-test-analyze cycles. This Boston-based, hybrid role will shape strategy, evaluation frameworks, and adoption of AI-enabled scientific workflows across discovery research.

The candidate will lead cross-functional teams, drive product leadership for AI-enabled workflows, and ensure governance and

Qualifications

• Ph.D. in a relevant scientific discipline.
• 8+ years applying computational chemistry/cheminformatics to drug discovery.
• Proven ability to translate opportunities into scalable AI capabilities.
• Experience leading cross-functional initiatives and influencing strategy.

Responsibilities

• Lead AI-enabled transformations across DMTA in small-molecule drug discovery.
• Develop and deploy AI co-scientists for knowledge synthesis, SAR analysis, and lead optimization.
• Define evaluation benchmarks and validation strategies for AI-enabled tools.
• Ensure responsible AI governance, data access controls, and operational guardrails.
• Drive adoption through scientist engagement and change leadership.

Skills

AI-enabled workflows

Computational chemistry

Cheminformatics

Molecular design

Machine learning

Data science

Product thinking

Cross-functional leadership

Education

Ph.D. in Computational Chemistry/related field

Job description

Job Description

Vertex is seeking a scientific leader to accelerate the application of AI and agentic systems across drug discovery. Working at the intersection of Computational Drug Design, project teams, Data & Methods, and Digital Technology & Engineering, this individual will leverage deep expertise in computational chemistry, cheminformatics, and AI-driven drug discovery to identify high-value opportunities across the design-make-test-analyze (DMTA) cycle and translate them into scientifically rigorous AI co-scientists that enhance compound design, knowledge synthesis, data interpretation, hypothesis generation, and decision-making. Although the primary focus will be small-molecule drug discovery, the successful candidate will also help extend relevant AI and agentic capabilities to protein therapeutics and other emerging therapeutic modalities. As a scientific leader, product owner, and trusted subject matter expert, the successful candidate will drive the strategy, development, evaluation, deployment, and adoption of AI-enabled scientific workflows. Success will be measured through broad scientist adoption, improved scientific productivity, faster and higher-quality decision-making, reduced time spent on information gathering and analysis, and measurable improvements in DMTA cycle efficiency.

This is a Boston based, hybrid position requiring 3 days/week onsite.

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.

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, optimize, 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.
• Recognized scientific leader with 8+ years of experience applying computational chemistry, cheminformatics, and related computational approaches to advance small-molecule drug discovery programs 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 organizations.
• 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 organizational transformation.
• Experience applying computational, data science, or AI approaches to protein therapeutics, biologics, or other therapeutic modalities is strongly preferred

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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:

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.

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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]