Associate Director, Computational Chemistry

Otsuka Pharmaceutical Companies (U.S.); Boston (MA); On-site; USD 170,000 - 210,000; Full time

Job summary

Jnana Therapeutics, a wholly owned subsidiary of Otsuka, is seeking an Associate Director of Computational Chemistry in Boston to apply structure-based drug design across the discovery process. You will collaborate with cross-functional teams to deliver models, predictions, and actionable insights that accelerate clinical development.

You will lead a team of computational scientists, develop new tools, and contribute to strategy with a focus on delivering high-quality designs and robust

Qualifications

• PhD in Computational Chemistry, Medicinal Chemistry, or related field with 7–10+ years of experience.
• Proven track record applying structure-based drug design to lead optimization.
• Experience supporting IND-enabling activities and regulatory filings.
• Deep expertise in molecular modeling and industry-standard tools.
• Strong understanding of SAR, potency, selectivity, ADME, and developability.
• Experience with X-ray crystallography and cryo-EM data translation.
• Ability to communicate complex results to non-computational scientists.

Responsibilities

• Act as computational lead on therapeutic projects to guide design.
• Collaborate with medicinal chemists to optimize compounds for potency and developability.
• Integrate structural insights with ADME and safety considerations.
• Present design recommendations to project teams and leadership.
• Stay current with advances in computational chemistry methods.

Skills

Structure-based design

Molecular modeling

Cross-functional collaboration

IND experience

Python scripting

Education

PhD in Computational Chemistry

PhD in Medicinal Chemistry

Tools

Molecular dynamics

Free energy calculations

Protein-ligand docking

X-ray crystallography

Cryo-EM data

Job description

About Us

Jnana Therapeutics, a wholly owned subsidiary of Otsuka Pharmaceutical, is a clinical-stage biotechnology company leveraging its next-generation RAPID chemoproteomics platform to discover medicines for highly validated, challenging-to-drug targets to treat diseases with high unmet needs. Jnana is focused on developing first- and best-in-class therapies to treat a wide range of diseases, including rare diseases and immune-mediated diseases. Jnana’s lead program, JNT-517, which targets an allosteric site on the phenylalanine transporter SLC6A19, is a potential first-in-class oral approach for the treatment of PKU, a rare genetic metabolic disease. Located in Boston, Jnana brings together scientific leaders in small molecule drug discovery and development, and a highly experienced management team. For more information, please visit www.jnanatx.com and follow us on Twitter/X and LinkedIn.

At Jnana, you'll join a diverse, passionate team dedicated to advancing therapies for challenging diseases. Our collaborative, purpose-driven culture fosters innovation, urgency, and belonging—making Jnana a great place to work!

About The Opportunity

As an Associate Director of Computational Chemistry, you will be integral to our drug discovery efforts, applying structure-based drug design methods to optimize molecules and guide medicinal chemistry strategy through all parts of the discovery process. This position will be working collaboratively in cross-functional teams to deliver models, predictions and actionable insights that accelerate progress toward clinical development.

You will join a team of highly skilled computational scientists eager to drive projects while developing and applying new tools and methods with exceptional scientific rigor. This is an exciting opportunity to join a growing computational chemistry team with the passion, resources and mandate to build a world-class group.

Responsibilities

• Act as the computational lead on therapeutic projects, conducting structure-based drug design efforts including molecular dynamics simulations, free energy perturbations, docking and structure analysis to guide medicinal chemistry synthesis priorities.
• Partner closely with medicinal chemists and project leads to interpret structural data, rationalize structure-activity relationships, and propose optimized compound designs that address potency, selectivity, and developability objectives.
• Contribute to lead optimization strategy by integrating structural insights with ADME, safety, and physicochemical property considerations to drive molecules toward clinical candidates.
• Communicate findings clearly to project teams and leadership, presenting design recommendations and structural insights that inform decision-making and advance programs.
• Stay current with advances in computational chemistry methods and the drug discovery environment, evaluating and implementing new approaches that enhance capabilities and improve results.

Required Qualifications & Skills

• PhD in Computational Chemistry, Medicinal Chemistry, or a related field with 7-10+ years experience and demonstrated ownership of cross-functional research projects.
• Demonstrated track record of applying structure-based drug design to successfully advance multiple drug discovery projects through lead optimization stages.
• Experience supporting IND-enabling activities and contributing to regulatory filings.
• Deep expertise in molecular modeling techniques and industry-standard tools for molecular dynamics simulations, free energy calculations, protein-ligand docking, structure analysis, binding mode prediction, and design hypothesis generation from structural data.
• Strong understanding of medicinal chemistry principles, structure-activity relationships, and the interplay between potency, selectivity, ADME properties, and developability.
• Experience working with diverse structural biology data including X-ray crystallography and cryo-EM and translating these data into actionable medicinal chemistry recommendations.
• Proven ability to work effectively in fast-paced, collaborative drug discovery teams and communicate complex computational results to non-computational scientists to advance molecules from lead optimization toward clinical development.

Preferred Qualifications

• Experience and expertise evaluating chemical patent literature.
• Programming or scripting skills (Python, Bash) for workflow automation and data analysis in a Linux-based environment.
• Familiarity with covalent drug design and modeling of covalent fragments.

Competencies

• Accountability for Results - Stay focused on key strategic objectives, be accountable for high standards of performance, and take an active role in leading change.
• Strategic Thinking & Problem Solving - Make decisions considering the long-term impact to customers, patients, employees, and the business.
• Patient & Customer Centricity - Maintain an ongoing focus on the needs of our customers and/or key stakeholders.
• Impactful Communication - Communicate with logic, clarity, and respect. Influence at all levels to achieve the best results for Otsuka.
• Respectful Collaboration - Seek and value others’ perspectives and strive for diverse partnerships to enhance work toward common goals.
• Empowered Development - Play an active role in professional development as a business imperative.

Come discover more about Otsuka and our benefit offerings; https://www.otsuka-us.com/careers-join-otsuka.

Otsuka 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.