Scientist II​/Senior Scientist, Computational Chemistry

Scientist II/Senior Scientist, Computational Chemistry

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  and follow us on Twitter/X and Linked In .

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!

Jnana Therapeutics is hiring for a Scientist II or Senior Scientist, this will be based on the candidate's alignment to the qualifications and experience for the role.

About the Opportunity

As a Scientist II in Computational Chemistry, you will contribute directly to structure-based drug design efforts across therapeutic programs. You will apply physics-based modeling and data-driven approaches to evaluate and optimize molecules from hit identification through clinical candidate nomination.

You will work closely with experienced computational chemists and cross-functional team members to generate models, test hypotheses, and deliver insights that guide medicinal chemistry strategy. This role is ideal for a scientist who is building independence in a collaborative drug discovery environment and eager to deepen their impact across projects.

It's an exciting opportunity to join a growing computational chemistry team with the passion, resources and mandate to build a world-class group.

Responsibilities

• Support structure-based drug design efforts for therapeutic projects, applying molecular modeling, docking, and structure analysis to guide chemistry synthesis priorities.
• Collaborate closely with medicinal chemists, biologists and structure biologists to design compounds that address potency, selectivity, and develop ability objectives.
• Apply physics-based methods (molecular dynamics, free energy calculations) alongside machine learning approaches to improve models and accelerate the design-make-test-analyze cycle for lead optimization.
• Contribute to the development of computational workflows and software that enables rapid analysis of compound designs across multiple programs.
• Stay current with advances in computational chemistry and machine learning for drug discovery to continuously improve methodologies and approaches.

Required Qualifications & Skills

• PhD in Computational Chemistry, Biophysics, Medicinal Chemistry, or a related field with 1-3+ years of postdoctoral and/or industry experience applying computational methods to drug discovery projects.
• Level will be determined based on demonstrated scope of experience, technical depth, independence, and readiness to contribute within a cross-functional drug discovery environment.
• Demonstrated experience in structure-based drug design, including molecular modeling, molecular dynamics simulations, free energy calculations, protein-ligand docking, and structure analysis to support lead optimization efforts.
• Demonstrated ability to work collaboratively in cross-functional drug discovery teams and clearly communicate computational results to experimental scientists.

Preferred Qualifications

• Understanding of medicinal chemistry principles, structure-activity relationships, and the factors that influence compound optimization toward clinical development.
• Experience working with structural biology data (X-ray crystallography, cryo-EM) and translating structural insights into design…