Senior Computational Chemist

Job Description

Job Description

The Company

Tupos Therapeutics is led by a seasoned team of drug hunters and developers with a proven track record of advancing transformative therapies. Our collective experience includes the discovery and development of first-in-class medicines such as vemurafenib and pexidartinib, along with multiple clinical-stage programs across diverse indications.

Our founding team helped pioneer a paradigm-shifting approach to small molecule drug discovery—anchoring structure-based drug design in the identification and validation of novel chemical scaffolds, an innovation widely recognized as a major contribution to the field. At Tupos, we extend this legacy by integrating cutting-edge computational chemistry, machine learning, and a growing arsenal of advanced chemistry toolkits. This multifaceted approach enables us to tackle some of the most persistent challenges in drug discovery and accelerate the path from program initiation to clinical entry. Headquartered near the geographic center of the San Francisco Bay Area—with an easy commute from the Peninsula, East Bay, and South Bay—Tupos is advancing a pipeline of novel therapies that target key immunological pathways—powered by a robust discovery platform and deep domain expertise.

The Opportunity

We are seeking an accomplished and highly motivated Computational Chemist to join our discovery team and lead the design of novel small molecules across multiple therapeutic programs. The ideal candidate will bring deep expertise in computational chemistry and structure-based drug design, a creative and mission-driven mindset, and a strong track record of advancing programs from early discovery through development candidate nomination. This is a high-impact role with the opportunity to shape discovery strategy, collaborate closely with cross-functional teams, and contribute significantly to the development of transformative therapies in a fast-paced environment.

Responsibilities

• Design novel small molecules with exceptional potency, selectivity, and drug-like properties by applying cutting-edge computational and machine learning techniques, modern structure-based drug design methods, and deep SAR insights to drive innovation and differentiation.
• Collaborate closely with cross-functional teams, including medicinal and synthetic chemistry, biology, DMPK, and translation medicine, to shape and execute discovery strategy, troubleshoot complex problems, and accelerate the progression of programs through key discovery milestones.
• Integrate and interpret diverse data streams, including biophysical/chemical, cellular, ADME, pharmacological, and structural biology data, to refine compound design hypotheses and enable rapid, data-driven decision-making in a fast-paced environment.
• Advance chemical series through iterative design cycles, proactively identifying and addressing liabilities related to efficacy, selectivity, pharmacokinetics, and developability, while contributing to intellectual property strategy and creation.
• Maintain fluency with emerging tools, technologies, and scientific literature in computational chemistry, machine learning, and drug discovery to bring forward novel approaches and continuously improve internal capabilities.
• Clearly and effectively communicate scientific insights, strategic recommendations, and project progress through written reports, team discussions, and internal or external presentations.

Qualifications

• Ph.D. in Computational Chemistry, Structural Biology, Medicinal Chemistry, Theoretical Chemistry, or a related discipline, with 5+ years of industry experience in small molecule drug discovery.
• Proven expertise in modern computer-aided drug discovery, including structure-based drug design, SAR analysis, and optimization of pharmacokinetic and physicochemical properties.
• Demonstrated success in advancing small molecule programs from hit identification through lead optimization and development candidate nomination.
• Experience collaborating in multidisciplinary teams and deep understanding of drug discovery principles, including ADME, pharmacology, and safety profiling, with the ability to synthesize complex datasets into clear, actionable design strategies.
• Proficient in using industry-standard computational tools and capable of scripting to automate workflows and analyze large datasets.
• Strong record of scientific communication, including authorship of publications, patent filings, and internal reports or presentations.
• Strategic thinker with excellent problem-solving skills, scientific curiosity, and the ability to thrive in a fast-paced, collaborative environment.
• Prior experience in immune-related indications or emerging therapeutic modalities such as targeted protein degradation or molecular glues is highly desirable.
• Familiarity with AI/ML approaches that can meaningfully accelerate small molecule discovery, such as generative modeling, property prediction, structure-focused learning, and integration of multi-modal datasets, is a strong plus.

Qualifications

• Ph.D. in Immunology or a related field, with 8+ years of relevant experience in a biopharma or biotechnology setting; experience in early drug discovery is strongly preferred.
• Deep expertise in immunology, with a strong understanding of immune signaling pathways, disease mechanisms, and immune modulation strategies.
• Demonstrated success in designing and interpreting in vitro, in vivo, and ex vivo studies to support target validation, mechanism-of-action, and biomarker development.
• Experience with a range of immunological assays (e.g., flow cytometry, cytokine profiling, cell co-culture systems) and disease-relevant models.
• Proven track record of advancing immunology-focused programs through early discovery to development candidate nomination.
• Strong leadership skills, with experience managing or guiding scientific teams and external collaborators.
• Effective cross-functional collaborator with the ability to influence decision-making across disciplines including chemistry, translational science, and clinical development.
• Excellent scientific communication skills, with experience presenting at internal governance meetings, external conferences, and contributing to peer-reviewed publications.

Benefits and Pay

The expected salary range for this position is $160,000 - $200,000. We encourage candidates of all levels to apply as there is sometimes flexibility on job level and responsibilities. Compensation and title will be based on a variety of factors, including experience, qualifications, and other job-related factors permitted by law. This position is also eligible for an annual bonus, equity, paid time off, and a benefits package. Benefits include company-subsidized medical, dental, and vision plans, and 401(K) matching. Employees may participate in benefit plans, subject to the terms and conditions of the applicable plans.

Tupos Therapeutics is an equal opportunity employer. It is our policy and practice to employ, promote, and otherwise treat any and all employees and applicants on the basis of merit, qualifications, and competence. The company's policy prohibits unlawful discrimination, including but not limited to, discrimination on the basis of Protected Veteran status, individuals with disabilities status, and consistent with all federal, state, or local laws.

To all recruitment agencies: Tupos Therapeutics does not accept agency resumes. Please do not forward resumes to our jobs alias or to Tupos Therapeutics employees. Tupos is not responsible for any fees related to unsolicited resumes.