Executive Director, AIRx Computational Chemistry

Cambridge, MA, USA|Onsite

Job Overview

Employment Type

Full-time

Compensation

Salary

Range $238,000.00 - $374,000.00

Benefits

Health Insurance

Dental Insurance

Vision Insurance

401(k) Plan

short-term disability

long-term disability

Paid Time Off

company holidays

Tuition Reimbursement

paid Volunteer Time Off

Job Description

Takeda Pharmaceutical Company Limited is a global, research and development-driven pharmaceutical company committed to discovering and delivering medicines that significantly improve the health and well-being of patients worldwide. With a focus on oncology, gastroenterology, neuroscience, rare diseases, and plasma-derived therapies, Takeda combines cutting-edge science with a patient-centric approach to accelerate drug discovery and delivery. The company values integrity, collaboration, and inclusion, fostering an environment where innovation and science thrive to bring transformative therapies to the market.

Based in Cambridge, MA, Takeda Research recently established the Discovery Automation & Robotics (DAR) group alongside the AI Research Accelerator (AIRx) to revolutionize drug discovery through AI, automation, and novel scientific methodologies. This initiative aims to expedite the journey of medicines to the clinic with enhanced speed and cost-efficiency by merging experienced drug hunters, advanced technological tools, and innovative operational models.

The Executive Director, Computational Chemistry role is a pivotal position within the AIRx team. Reporting directly to the Head of AIRx, this role is at the forefront of integrating in silico molecular design with AI-driven technologies to transform drug discovery. The position involves leveraging generative AI, structure-based drug design, machine learning predictive models, and free energy perturbation techniques to rapidly iterate design-make-test-analyze (DMTA) cycles essential for identifying and advancing new therapeutic candidates. This role will directly influence critical decision-making in molecular design, selecting candidates for synthesis, prioritizing projects, and progressing promising compounds to clinical trials.

This is a highly hands-on scientific leadership role requiring a blend of deep computational expertise and collaborative skills to work effectively with medicinal chemists and other interdisciplinary teams. The Executive Director will lead virtual screening campaigns, ADMET property predictions, and selectivity assessments, while also contributing to the development and enhancement of computational workflows to boost efficiency and reproducibility of discoveries. The role also involves interpreting X-ray crystallography and cryo-electron microscopy structural biology data to inform computational strategies.

Candidates will have the opportunity to shape the future of AI-powered drug discovery within a unique incubator environment that balances autonomy with the resources of a large pharmaceutical company. Takeda provides a competitive salary range for this role, from $238,000 to $374,000 annually, reflecting the individuals experience and expertise, alongside comprehensive benefits including medical, dental, vision insurance, retirement plans, paid time off, and well-being programs.

The position is classified as hybrid under Takeda’s Flexible Work policies, allowing a blend of remote and on-site work in Boston, Massachusetts. Takeda is committed to diversity, equity, and inclusion, providing equal employment opportunities to all qualified candidates irrespective of race, gender, age, disability, or protected veteran status. Join Takeda to be part of a future-focused organization that leverages science, technology, and human talent to transform patients’ lives worldwide.

Job Requirements

PhD in computational chemistry, cheminformatics, biophysics, or related discipline
12-15+ years of drug discovery experience
proficiency in molecular docking, MD simulation, FEP, QSAR/ADMET modeling
strong Python coding skills
experience with structure-based drug design
experience interpreting crystallography or cryo-EM data
ability to work collaboratively across disciplines
authorization to work in the US
ability to work in a hybrid environment based in Cambridge, MA

Job Qualifications

PhD in computational chemistry, cheminformatics, biophysics, or closely related discipline
12-15+ years of drug discovery experience with demonstrated track record of computational impact on programs
proficiency across computational tools including molecular docking, MD simulation, FEP, QSAR/ADMET modeling
strong coding skills (Python required)
experience building and deploying ML models in a drug discovery context
experience with structure-based drug design and ability to interpret crystallography or cryo-EM data
experience applying generative AI or large language models to molecular design preferred
collaborative, communicative, and comfortable at the wet/dry scientific interface

Job Duties

Apply generative AI, structure-based design, free energy perturbation, and predictive ML models to design and prioritize chemical matter
partner closely with medicinal chemists to translate computational outputs into actionable synthesis priorities
lead and oversee virtual screening campaigns, ADMET predictions, and selectivity assessments to inform and accelerate design decisions
contribute to building and refining AI/ML model training datasets from AIRx experimental outputs
develop and maintain computational workflows that increase team speed and reproducibility
interpret and integrate structural biology data including X-ray and cryo-EM into computational design strategies
communicate complex computational findings clearly to cross-disciplinary colleagues and governance forums
stay current with advances in generative AI, protein structure prediction, and ML methods and proactively apply new approaches