Computational Chemistry Lead

Astellas Pharma; Cambridge (MA); On-site; USD 119,000 - 170,000; Full time

Benefits offered by this job

Medical, Dental & Vision

401(k) match

Life insurance

Annual bonus & incentives

Long-term incentives

Company vehicle

Referral bonus

Job summary

Astellas Pharma is seeking a Computational Chemist in Cambridge, MA to support drug discovery using advanced computational chemistry, AI-driven design, and CRO partnerships. The candidate will collaborate across medicinal chemistry, biology, pharmacology, and data science to optimize small molecules and drive project success.

The role emphasizes on-site work in Cambridge, MA with opportunities to lead strategic initiatives and contribute to multiple therapeutic areas, staying current with

Qualifications

• Ph.D. in Computational Chemistry, Cheminformatics, Medicinal Chemistry, or related field or MS with industry experience.
• Experience in computational support of small-molecule drug discovery.
• Familiarity with AI-driven drug design and software tools.
• Strong understanding of organic and synthetic chemistry concepts.
• Experience managing CRO relationships and external collaboration.

Responsibilities

• Apply molecular modeling, docking, MD, and design to guide compound optimization.
• Use ML/AI to analyze SAR, ADME/Tox and predict compound behavior.
• Develop generative models and predictive analytics for design.
• Manage data pipelines and curate chemical libraries for SAR/ADME analyses.
• Lead or co-lead projects with clear goals and plans.
• Collaborate with medicinal chemistry, biology, and pharmacology teams.
• Oversee CRO execution and onboarding to improve cost-efficiency.

Skills

Molecular Modeling

Structure-based design

Molecular docking

Molecular dynamics

QM/MM

Homology modeling

Pharmacophore modeling

Virtual screening

Cheminformatics

Data Science

Machine learning

Python

KNIME

Scripting

Education

Ph.D. in Computational Chemistry or related field

M.S. with 5+ years of industry experience

Tools

Schrödinger

MOE

OpenEye

Rosetta

Python

Pipeline Pilot

KNIME

Job description

About Astellas

Astellas is a global life sciences company committed to turning innovative science into VALUE for patients. We provide transformative therapies in disease areas that include oncology, ophthalmology, urology, immunology and women's health. Through our research and development programs, we are pioneering new healthcare solutions for diseases with high unmet medical need. Learn more at Astellas.com.

Computational Chemistry

Are you driven to make a real difference in the lives of patients? We’re seeking passionate individuals who thrive in dynamic environments, embrace new ideas, and aren’t afraid to take intelligent risks. People who act with unwavering integrity and are deeply committed to making a tangible impact.

Purpose & Scope: This role supports drug discovery efforts by applying advanced computational chemistry techniques to design and optimize small‑molecule therapeutics. The position requires close collaboration with internal teams and external CROs to accelerate candidate selection and improve research productivity. The Computational Chemist will contribute to strategic decisions and innovation across multiple therapeutic areas.

Role And Responsibilities

• Computational Drug Design: Apply molecular modeling, docking, molecular dynamics, homology modeling, and structure‑based design to guide compound optimization
• Use cheminformatics and machine learning tools to analyze SAR, ADME/Tox profiles, and predict compound behavior.
• Develop generative models, reinforcement learning pipelines, and predictive analytics for compound design and optimization
• Curate chemical libraries, manage data pipelines, and support SAR/ADME analysis
• Serve as lead or co‑lead in projects, setting project goals and defining plans
• Drug Design & Synthesis: Design novel compounds based on ADME and SAR principles; optimize lead molecules for potency, selectivity, and pharmacokinetics.
• Data Analysis & Reporting: Analyze large datasets from simulations and experimental data with scientific rigor; interpret computational results and prepare detailed research reports and present findings internally and externally to technical and non‑technical audiences.
• Cross‑functional Collaboration: Work closely with medicinal chemistry, biology, pharmacology, protein science, and preclinical teams to ensure drug candidates meet efficacy and safety standards. Participate in program‑related meetings and contribute strategic insight
• Intellectual Property: Identify and protect IP through patent filings and strategic documentation. Ensure accurate documentation of compound synthesis and project data
• Foster a collaborative, transparent, and creative team environment that drives innovation and invention. Close partnership with colleagues in Japan is expected.
• Technology Integration: Explore and apply cutting‑edge technologies and global scientific trends to enhance research capabilities
• Stay current with scientific literature and emerging technologies
• Manage team priorities and resources in alignment with the company’s overall I‑Lab strategy and objectives.

CRO Management

• Oversee computational chemistry execution at CROs, including troubleshooting and performance enhancement
• Evaluate and onboard new CROs to improve cost‑efficiency and research quality
• Maintain weekly communication and productivity tracking with CRO teams

Required Qualifications

• Ph.D. in Computational Chemistry, Cheminformatics, Medicinal Chemistry, or related field; or M.S. with 5+ years of industry experience
• Proven experience in computational support of small‑molecule drug discovery
• Familiarity with AI‑driven drug design
• Proficiency in software packages such as Schrödinger, MOE, OpenEye, Rosetta, and scientific programming (Python, Pipeline Pilot)
• Strong understanding of organic and synthetic chemistry concepts
• Experience managing CRO relationships and external collaboration
• Deep understanding of advancements in drug discovery, emerging technologies, and industry trends, and experience applying this knowledge to enhance research strategies

Technical Expertise

• Molecular Modeling & Simulation: Proficient in structure‑based drug design (SBDD), including molecular docking, molecular dynamics (MD), and free energy perturbation (FEP)
• Skilled in homology modeling, pharmacophore modeling, and quantum mechanics/molecular mechanics (QM/MM) methods
• Experienced in cryptic pocket identification and virtual screening for challenging targets
• Cheminformatics & Data Science: Applies cheminformatics tools to analyze structure‑activity relationships (SAR), ADME/Tox profiles, and compound clustering
• Uses machine learning (ML) and AI‑driven platforms for compound prioritization, generative design, and predictive modeling
• Familiar with scripting languages like Python and platforms such as Schrödinger, MOE, and KNIME
• Drug Discovery Integration: Designs and optimizes small molecules for potency, selectivity, and pharmacokinetics
• Collaborates with medicinal chemists, biologists, and pharmacologists to guide compound progression from hit to lead

Skills

• Strong collaboration and teamwork abilities
• Excellent oral and written communication in English
• Strategic thinking and problem‑solving capabilities
• Strong communication and influencing skills
• Highly collaborative win‑win mindset is essential

Working Environment

• This position is based in Cambridge, MA and will require on‑site work

What awaits you at Astellas?

• Global collaboration: Become part of a connected global business of like‑minded life‑science leaders, all dedicated to improving patients’ lives worldwide. Real‑world patient impact: Contribute to transformative therapies that reach patients around the world, knowing your work makes a difference every day.
• Relentless Innovation: Join a company at the forefront of scientific breakthroughs, where you’ll have the opportunity to shape the future of healthcare
• A Culture of Growth: Chart your own course within a supportive environment that values your contributions, champions your development, and empowers you to pursue your passions

Values

Innovation, Integrity and Impact sit at the heart of what we do

Behaviors

We come together as ‘One Astellas’, working with courage and a sense of urgency. We are outcome focused and consistently take accountability for our personal contribution

Salary Range

$119,000-$170,000 (Final compensation will be determined based on a variety of factors, including but not limited to skills, experience and organizational equity considerations)

Benefits

• Medical, Dental and Vision Insurance
• Generous Paid Time Off options, including Vacation and Sick time, plus national holidays including year‑end shut down
• 401(k) match and annual company contribution
• Company paid life insurance
• Annual Corporate Bonus and Quarterly Sales Incentive for eligible positions
• Long Term Incentive Plan for eligible positions
• Company fleet vehicle for eligible positions
• Referral bonus program

Astellas is committed to equality of opportunity in all aspects of employment

EOE including Disability/Protected Veterans