Senior Principal Scientist, Agentic Systems Development for Drug Discovery

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

Benefits offered by this job

Medical, dental, and vision benefits

Paid time off

Educational assistance programs

Commuting subsidy

Matching charitable donations

401(k)

Job summary

Vertex Pharmaceuticals Incorporated seeks a Senior Principal Scientist to lead the development and deployment of agentic AI systems for drug discovery. The role spans small molecules and proteins, driving AI-enabled scientific workflows with collaboration across computational sciences, software engineering, and Digital Technology & Engineering.

This Boston-based, hybrid position requires onsite work three days per week. A Ph.D.

Qualifications

• Ph.D. in Computational Chemistry, Cheminformatics, or a related scientific discipline.
• 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 or platforms.
• Proven ability to translate scientific opportunities into scalable computational or AI capabilities with measurable impact.
• Experience working across discovery research, computational sciences, data science, and engineering.

Responsibilities

• Translate scientific requirements into agentic AI solutions for autonomous reasoning and planning.
• Build, test, and deploy AI-enabled solutions supporting drug discovery across modalities.
• Collaborate with computational scientists, software engineers, and cross-functional teams.
• Apply software engineering, DevOps, and compliance best practices for production-grade AI systems.
• Design testing, evaluation, and validation strategies for agentic AI systems.
• Contribute to innovation efforts to leverage agentic and generative AI in research programs.
• Stay current with emerging agentic AI patterns and prototype new capabilities.

Skills

Agentic AI

Python programming

Machine learning

CI/CD

DevOps practices

Scientific software development

Stakeholder management

Cross-functional collaboration

Education

Ph.D. in Computational Chemistry or Cheminformatics

8+ years in scientific software development

Experience with AI-enabled scientific products

Tools

Cheminformatics tools

Drug discovery platforms

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

#LI-KM1

#LI-Hybrid

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:

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.

#LI-Hybrid

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]