Head of Automated Small Molecule Synthesis

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Job Description

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.

Objective / Purpose:

The Research Scientific Director, Head of Small molecule Automation, is based in Cambridge, MA, within the R&D — Research division, specifically supporting Takeda’s Digital Discovery & Development Engine. This full-time Director-level role is instrumental in building and leading the automation of small molecule synthesis for Takeda’s Discovery Automation & Robotics (DAR) initiative to implement highly efficient, AI-integrated DMTA (Design–Make–Test–Analyze) cycles toward rapid and reliable small molecule discovery.

The Head of Small Molecule Automation leads the strategy, design, and execution of small molecule synthesis using fully automated, robotic platforms to accelerate decision-making across Takeda’s discovery portfolio by quickly and reliably generating compound sets for testing. The role collaborates closely with medicinal chemistry, in-vitro pharmacology, DMPK, data science/AI/computational chemistry, and automation engineering to ensure seamless integration of compound synthesis with AI-driven design, and includes integrating retrosynthetic planning, route design, and advanced chemical reaction miniaturization capabilities.

Accountabilities:

• Define and execute the automation strategy for small-molecule synthesis, aligning platform capabilities with organizational discovery and development goals and the Lab of the Future roadmap.
  • Prioritize and sequence automation investments in equipment, software, and talent based on scientific impact, throughput gains, and cost-to-value ratios.
  • Promote the adoption of digital-first and automated approaches across the research community as a change champion.

• Establish a closed-loop DMTA vision by integrating robotics, digital data capture, and AI/ML to boost synthesis throughput, reduce cycle times, and enhance decision quality.
  • Design end-to-end automated workflows for reaction scouting, parallel synthesis, scale-out, and purification (e.g., flash/Prep-HPLC) to ensure reproducibility and traceability.
  • Standardize method libraries and digital SOPs, covering reaction templates, purification methods, and analytical routines, to enable rapid and consistent deployment across programs.
  • Continuously evaluate and integrate new technologies such as liquid-handling robotics, continuous flow, microreactors, smart reactors, and generative chemistry tools.
  • Accelerate DMTA cycles through high-throughput experimentation (HTE), parallel synthesis arrays, flow chemistry, and automated purification integrated with ELN/LIMS and scheduling/orchestration systems for efficient, low-touch labs.
  • Establish and refine a vision for fully integrated workflows that encompass compound design, purification, QC data capture, analysis, and sample preparation for testing.
  • Define, track, and report KPIs such as workflow efficiency, data accessibility, and cycle time improvements.
  • Encourage method innovation, including novel reaction classes on automation, greener conditions, and continuous processing.
• Drive reliability engineering, preventive maintenance, and improvements
  • Integrate EHS, machine safety, and cybersecurity
  • Ensure up-time with scheduled maintenance, spares management, incident handling, and corrective action.
  • Scale workflows from prototype to routine and maintain lab safety and compliance for automated operations.
  • Oversee change control, validation, risk assessment, and conduct drills and post-mortems.
• Engage externally through contributions to patents, publications, and presentations that highlight platform advancements, and by active participation in consortia and conferences to share knowledge and gain insights to remain at the forefront of best practices.

• Contribute to data governance practices that promote longitudinal learning across Takeda’s discovery portfolio.
• Uphold Takeda’s values of Integrity, Fairness, Honesty, and Perseverance in all scientific and operational activities.

Education & Competencies (Technical and Behavioral):

• Expected: Ph.D. in Organic or Medicinal Chemistry (or related field) with 10+ years of experience; or M.S. with 16+ years of experience; or B.S. with 18+ years of experience in pharmaceutical or biotech R&D, including small-molecule discovery.
• Deep medicinal chemistry knowledge, including SAR, SBDD, cheminformatics, and ADME/PK data interpretation.
• 10+ years building and scaling lab or chemical process automation, and 5+ years leading cross-functional R&D teams.
• Proficiency with automated synthesis platforms, including robotic reaction screening, parallel synthesis, and purification systems.
• Experience with AI-driven DMTA and autonomous design-make loops and experiment planners.
• Familiarity with scheduling software, LIMS/ELN, and data pipeline tools used in automated labs.
• Strong leadership, managing and developing scientific teams at the senior scientist/principal scientist level.
• Exceptional written and verbal communication, with ability to influence at the Executive Director and VP levels.
• Demonstrated ability to drive change and transformation in complex, global R&D organizations.

ADDITIONAL INFORMATION

• The position will be based in Cambridge, MA.

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices. 

For Location:

Boston, MA

U.S. Base Salary Range:

$177,000.00 - $278,080.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location. 

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation. 

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Full time

Job Exempt

Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.