Associate Director, Computational Chemistry

Otsuka Pharmaceutical Co., Ltd; Boston (MA); On-site; USD 154,800 - 222,525; Full time

Benefits offered by this job

Comprehensive medical coverage

401(k) match

Flexible time off

Job summary

Otsuka Pharmaceutical Co., Ltd is seeking an Associate Director of Computational Chemistry in Boston. This role involves leading structure-based drug design efforts, collaborating with research teams to optimize drug candidates, and communicating complex findings. The ideal candidate possesses a PhD and significant experience in drug discovery. A competitive salary and benefits package are offered, making this an attractive opportunity in the thriving biotech field.

Qualifications

• 7-10+ years experience in drug discovery.
• Track record in structure-based drug design.
• Experience supporting IND-enabling activities.

Responsibilities

• Lead structure-based drug design efforts.
• Collaborate with medicinal chemists.
• Communicate findings and design recommendations.

Skills

Molecular dynamics simulations

Structure-based drug design

Medicinal chemistry principles

Protein-ligand docking

Education

PhD in Computational Chemistry or related field

Tools

Python

Bash

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.

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.

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

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.

Compensation

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.

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.
• Generous 401(k) match.
• Flexible time off, paid holidays, and paid leave programs as well as other company provided benefits.

Equal Opportunity Statement

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.