Medicinal Chemistry Program Leader

Takeda Pharmaceutical; Boston (MA); Hybrid; USD 154,000 - 243,000; Full time

Benefits offered by this job

Hybrid work model

Job summary

Takeda in Boston, MA seeks an experienced Medicinal Chemistry Program Leader (Associate Director level) to drive discovery programs from hit-to-lead and nominate candidates. You will lead design, synthesis, and progression of compounds, coordinating internal chemists and CRO partners, delivering milestones within budget.

You will mentor junior chemists, apply cutting-edge design and automation, and contribute to IP while collaborating with biology, pharmacology, and DMPK teams in a hybrid work

Qualifications

• Education and experience: PhD in Organic Chemistry, Medicinal Chemistry, or related discipline with 6+ years in pharma/biotech medicinal chemistry, or MS with 12+ years, or BS with 14+ years.
• Proven track record in discovery programs advancing compounds to candidate nomination or clinic.
• Strong understanding of medicinal chemistry principles, SAR, drug design, and PK/PD relationships.
• Ability to lead cross-functional project teams and drive execution against timelines.
• Experience directing and mentoring chemists, including CRO partnerships.
• Excellent verbal and written communication skills to convey complex science.
• Analytical, proactive problem-solving abilities and adaptability.

Responsibilities

• Lead medicinal chemistry programs from hit identification through lead optimization and candidate nomination.
• Design and prioritize compounds using SAR, structure-based and computational design, optimizing potency, selectivity, ADME, and safety.
• Serve as chemistry lead on cross-functional teams with biology, pharmacology, DMPK, and toxicology; communicate progress and risks.
• Direct internal chemists and CRO-based teams, set priorities, review plans and data, ensure timely delivery within budget.
• Collaborate with discovery scale-up and process chemistry for tractable synthesis and material supply for in vivo studies.
• Prepare data packages and recommendations for program reviews, go/no-go decisions, and nomination.
• Mentor junior chemists and share best practices in design, synthesis, and data interpretation.
• Apply new methodologies and technologies (computational design, parallel synthesis, automation) to accelerate cycles.
• Contribute to invention disclosures and patent filings; maintain accurate scientific records.

Skills

Team leadership

Structure-based design

SAR analysis

Cross-functional leadership

Mentoring

Communication

Education

PhD in Organic/Medicinal Chemistry

Job description

Job Description

About the role:

We are seeking a hands‑on medicinal chemistry leader to drive the execution of our discovery programs as a Medicinal Chemistry Program Leader at the Associate Director level. In this role, the successful candidate will lead the day‑to‑day design, synthesis, and progression of compounds for one or more programs, translating target and biology strategy into potent, selective, and developable molecules. They will serve as the chemistry lead on cross‑functional project teams, direct the work of internal chemists and external partners such as contract research organizations (CROs), and be accountable for delivering program milestones from hit‑to‑lead through candidate nomination.

How you will contribute:

• Program Execution: Lead the execution of medicinal chemistry programs from hit identification through lead optimization and candidate nomination, delivering against agreed milestones, timelines, and candidate criteria.
• Compound Design and SAR: Design and prioritize compounds using structure‑activity relationships, structure‑based and computational design, and multiparameter optimization of potency, selectivity, ADME, and safety properties.
• Project Team Leadership: Serve as the chemistry lead on cross‑functional project teams with biology, pharmacology, DMPK, and toxicology, communicating progress, risks, and recommendations clearly to team and management.
• Team and CRO Oversight: Direct the work of internal chemists and CRO‑based teams, setting priorities, reviewing synthetic plans and data, and ensuring timely, high‑quality delivery within program budget and resources.
• Scale‑Up Partnership: Work with discovery scale‑up and process chemistry colleagues to ensure synthetic tractability and timely supply of material for in vivo and other key studies.
• Decision‑Making and Governance: Prepare data packages and recommendations for program reviews and portfolio decisions, including go/no‑go and candidate nomination.
• Mentorship: Mentor and develop junior chemists, sharing best practices in design, synthesis, and data interpretation.
• Innovation: Apply new methodologies and technologies, such as computational design, parallel synthesis, and automation, to improve the speed and quality of design‑make‑test‑analyze cycles.
• Intellectual Property: Contribute to invention disclosures and patent filings, and maintain accurate, well‑documented scientific records.

Qualifications:

• Expected education and experience: PhD in Organic Chemistry, Medicinal Chemistry, or a related discipline, with 6+ years experience, or MS with 12+ years experience, or BS with 14+ years experience of pharmaceutical or biotechnology industry experience in medicinal chemistry.
• Proven track record of contributing to or leading discovery programs that advanced compounds to candidate nomination or the clinic.
• Technical Expertise: Strong understanding of medicinal chemistry principles, SAR, drug design, and the interplay of potency, ADME, pharmacokinetics, and physical properties.
• Project Leadership: Demonstrated ability to lead cross‑functional project teams and drive execution against timelines and milestones.
• Leadership Skills: Experience directing, mentoring, and developing chemists, including work with external CRO partners.
• Communication: Excellent verbal and written communication skills, with the ability to explain complex scientific concepts to a broad audience.
• Problem‑Solving and Adaptability: Strong analytical skills, a proactive approach to challenges, and the ability to adapt to changing priorities and make sound decisions with incomplete data.

Preferred Qualifications:

• Experience: Experience in a large pharmaceutical or biotechnology company, including managing programs across internal and external sites.
• Therapeutic Areas: Experience in oncology, neuroscience, or inflammation.
• Modalities: Experience with small‑molecule modalities beyond traditional compounds, such as macrocycles, peptides, or degraders.
• Publications and Patents: Publication record in medicinal chemistry or related fields, and named inventor on patent filings.

This position is currently classified as “hybrid” in accordance with Takeda’s Hybrid and Remote Work policy.

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:

$154,400.00 - $242,550.00

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.

For information about our benefits, please click here.

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

YesIt 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.