Senior Scientist, Computational Chemistry

Otsuka Pharmaceutical Co., Ltd; Boston (MA); On-site; USD 124,000 - 178,000; Full time

Benefits offered by this job

Medical benefits

401(k) match

Tuition reimbursement

Paid holidays

Job summary

Jnana Therapeutics, based in Boston, seeks a Senior Scientist in Computational Chemistry to drive drug-design innovations from hit identification through nomination of clinical candidates. You will implement computational approaches that blend physics-based methods with machine learning, advancing a world-class computational chemistry team.

You will lead independent research, collaborate across disciplines, and build workflows that accelerate lead optimization while maintaining scientific rigor

Qualifications

• PhD in Computational Chemistry, Biophysics, Medicinal Chemistry, or related field with substantial industry experience (4+ years) and demonstrated independence.
• Level determined by independence, depth, ownership, and cross-functional influence in drug discovery.
• Strong experience in structure-based drug design, including modeling, dynamics, free energy, docking, and analysis to support lead optimization.

Responsibilities

• Design and execute molecular modeling, docking, and structure analysis to guide synthesis and support structure-based drug design.
• Collaborate with medicinal chemists, biologists, and structure biologists to optimize potency, selectivity, and developability.
• Apply physics-based methods (MD, free energy) alongside ML to improve models and speed up design-make-test-analyze cycles.
• Contribute to development of computational workflows and software for rapid analysis across programs.
• Stay current with advances in computational chemistry and ML for drug discovery to continuously improve methodologies.

Skills

Molecular modeling

Molecular dynamics

Free energy calculations

Protein-ligand docking

Python

Machine learning

Team collaboration

Independent research

Education

PhD in Computational Chemistry or related field

Tools

Molecular dynamics software

Docking tools

Structure analysis tools

Job description

As a Senior Scientist in Computational Chemistry, you will help drive innovation in how we design and optimize drug candidates. You will independently design and implement computational approaches that directly influence project direction from hit identification through clinical candidate nomination. You will apply best practices from machine learning approaches that integrate with physics-based methods to accelerate the design cycle for therapeutic programs. 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

• Design and execute molecular modeling, docking, and structure analysis to guide chemistry synthesis priorities and support structure-based drug design efforts for therapeutic projects.
• Collaborate closely with medicinal chemists, biologists and structure biologists to design compounds that address potency, selectivity, and developability 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 substantial industry experience (4+ years) and demonstrated independence of research projects in a cross-functional drug discovery environment.
• Level will be determined based on demonstrated independence, technical depth, project ownership, and ability to influence in a cross-functional drug discovery environment.
• Strong 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 hypotheses.
• Experience with AI toolkits for drug discovery to apply machine learning, multi-agent systems or active learning approaches to improve compound designs.
• Programming proficiency in Python and experience with machine learning frameworks (scikit-learn, PyTorch, TensorFlow, or similar).
• Experience with cloud computing platforms (AWS) and Linux environments.

Minimum $123,600.00 - Maximum $177,675.00, 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.

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.

Jnana Therapeutics, a wholly owned subsidiary of Otsuka Pharmaceutical, is a clinical-stage biotechnology company leveraging its next-generationRAPIDchemoproteomics 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. 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 visitwww.jnanatx.comand follow us onTwitter/XandLinkedIn. 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!