Associate Director, Medicinal Chemistry, Targeted Protein Degradation

Otsuka Pharmaceutical Co., Ltd.; Boston (MA); On-site; USD 155,000 - 223,000; Full time

Job summary

Jnana Therapeutics is seeking an experienced medicinal chemist to lead the Targeted Protein Degradation (TPD) chemistry strategy. You will guide multiple programs and drive the next-generation degradation platform from the ground up.

The role emphasizes scientific leadership, cross-functional collaboration, and the development of novel modalities in degradation chemistry within a Boston-area team.

Qualifications

• Ph.D. in Chemistry or related field with extensive industry experience in medicinal chemistry and 8+ years in industry.
• Demonstrated success leading one or more targeted protein degradation programs with heterobifunctional molecules to development candidates.
• Deep understanding of SAR, linker design, and bifunctional molecule optimization.
• Strong knowledge of E3 ligase biology and degrader mechanisms.
• Experience cross-functional with ADME/DMPK, biology, and computational chemistry.

Responsibilities

• Define and implement the company’s TPD chemistry strategy, including degrader design principles, toolbox development, and platform evolution.
• Lead TPD chemistry efforts on assigned programs and contribute to platform strategy and development candidate selection.
• Establish linker and building block strategies, including sourcing and synthesis guidance for E3 ligase ligands and linkers.
• Partner with ADME/DMPK to shape property and developability strategies for TPD molecules.
• Explore new heterobifunctional modalities beyond CRBN/VHL, including extracellular protein degradation.

Skills

TPD leadership

Targeted protein degradation

Degrader design

Cross-functional leadership

SAR understanding

ADME/DMPK collaboration

Parallel synthesis

Education

Ph.D. in Chemistry

Tools

Parallel synthesis

Direct-to-biology chemistry

Job description

Position Summary

We are seeking an experienced medicinal chemist to lead our Targeted Protein Degradation (TPD) chemistry strategy. This individual will bring prior leadership experience advancing TPD programs and will be responsible for shaping and executing the company’s degradation platform.

This role combines scientific leadership and strategic direction with the opportunity to both guide multiple programs and directly lead a TPD project. Importantly, this individual will play a foundational role in expanding the company’s capabilities into next-generation degradation modalities (e.g. extracellular proteins), helping define platform direction from the ground up.

Key Responsibilities:

Scientific & Strategic Leadership:

• Define and implement the company’s TPD chemistry strategy, including degrader design principles, toolbox development, and platform evolution.
• Work with chemistry leads and project teams to lead TPD chemistry efforts on assigned programs, contributing to platform strategy and advancing molecules toward development candidate selection..
• Establish linker and building block strategies, including guiding sourcing and synthesis of E3 ligase ligands and linkers.
• Partner with ADME/DMPK teams to shape property and developability strategies specific to TPD molecules.
• Help define and initiate new heterobifunctional modalities beyond CRBN/VHL based degraders, including ongoing efforts in extracellular protein degradation.

Team Leadership & Cross-Functional Collaboration:

• Mentor and oversee a scientist responsible for establishing a parallel synthesis capability to accelerate lead discovery.
• Collaborate closely with medicinal chemistry, computational chemistry and ADME leads across programs.
• Serve as the internal TPD expert, influencing multi-project direction and decision-making.

Execution & Innovation:

• Drive rapid iteration cycles through efficient synthetic design and prioritization.
• Incorporate emerging advances in TPD modalities, linker chemistry, and E3 biology.
• Play a key role in building the next-generation degradation platform, including evaluating and implementing novel modalities (e.g., extracellular protein degradation, molecular glues, and beyond).
• Help build scalable workflows and infrastructure to support platform productivity.

Qualifications:

Required:

• Ph.D. in Chemistry or related field with extensive industry experience in medicinal chemistry with 8+ years of industry
• Demonstrated success leading one or more targeted protein degradation programs with heterobifunctional molecules through to a development candidate.
• Deep understanding of SAR, linker design, and bifunctional molecule optimization.
• Strong knowledge of E3 ligase biology and degrader mechanisms
• Experience working cross-functionally with ADME/DMPK, biology, and computational chemistry.

Leadership Profile:

• Track record of scientific leadership and program ownership.
• Ability to operate at both strategic and hands-on levels.
• Strong collaborator capable of influencing across disciplines.
• Experience mentoring scientists and building capabilities.

Preferred:

• Experience establishing or scaling a TPD or proximity-based pharmacology platform.
• Familiarity with emerging heterobifunctional modalities.
• Familiarity with parallel synthesis and direct-to-biology chemistry workflows.

Minimum $154,800.00 - Maximum $222,525.00, plus incentive opportunity: The range shown represents a typical pay range or starting pay for individuals who are hired in the role to perform in the United States. Other elements may be used to determine actual pay such as the candidate’s job experience, specific skills, and comparison to internal incumbents currently in role. Typically, actual pay will be positioned within the established range, rather than at its minimum or maximum. This information is provided to applicants in accordance with states and local laws.

Application Deadline

This will be posted for a minimum of 5 business days.

Company benefits:

Comprehensive medical, dental, vision, prescription drug coverage, company provided basic life, accidental death & dismemberment, short-term and long-term disability insurance, tuition reimbursement, student loan assistance, a generous 401(k) match, flexible time off, paid holidays, and paid leave programs as well as other company provided benefits.

https://www.jnanatx.com/join-us/

Disclaimer:

This job description is intended to describe the general nature and level of the work being performed by the people assigned to this position. It is not intended to include every job duty and responsibility specific to the position. Jnana Therapeutics reserves the right to amend and change responsibilities to meet business and organizational needs as necessary.

Jnana Therapeutics is an equal opportunity employer. All qualified applicants are encouraged to apply and will be given consideration for employment without regard to race, color, sex, gender identity or gender expression, sexual orientation, age, disability, religion, national origin, veteran status, marital status, or any other legally protected characteristic.

If you are a qualified individual with a disability or a disabled veteran, you may request a reasonable accommodation, if you are unable or limited in your ability to apply to this job opening as a result of your disability. You can request reasonable accommodations by contacting Accommodation Request.