Principal/ AD Medicinal Chemist

Deep Origin Inc.; South San Francisco (CA); Hybrid; USD 180,000 - 240,000; Full time

Benefits offered by this job

Competitive compensation

Equity participation

Remote-friendly culture

Flexible hours

Job summary

Deep Origin Inc. is seeking a Principal/AD Medicinal Chemist to lead small molecule drug discovery from hit identification through IND-enabling studies.

This senior, hands-on role requires deep expertise in medicinal chemistry and cross-functional leadership, directing work to CROs as needed. The candidate will integrate AI-driven approaches into workflows, guide internal teams and external partners, and help shape strategy for advancing programs toward development candidates in a

Qualifications

• PhD in Organic Chemistry or related field with 3–8 years of medicinal chemistry experience.
• Proven track record advancing drug discovery to Hit-to-Lead and Lead Optimization milestones.
• Expertise in synthetic organic chemistry including modern methods and mechanisms.
• Strong experience in structure-based and ligand-based drug design.
• Ability to optimize compounds for potency, selectivity, and DMPK/safety.
• Experience managing external CROs and collaborating across disciplines.
• Excellent communication of complex scientific concepts.

Responsibilities

• Propose and independently drive medicinal chemistry strategies from hit ID to lead optimization.
• Lead chemistry efforts within cross-functional teams with biology, DMPK, tox, and computational science.
• Guide synthesis of novel compounds using structure- and ligand-based approaches to optimize potency and developability.
• Interpret SAR and integrative data to drive design and progression.
• Incorporate AI-driven and computational insights into design strategies.
• Mentor internal chemists and external partners.
• Manage external CRO partnerships to ensure high-quality delivery of chemistry objectives.
• Communicate program status, risks, and recommendations to senior leadership.
• Contribute to patent strategies, publications, and internal reports.

Skills

Synthetic organic chemistry

Structure-based design

Ligand-based design

DMPK/safety optimization

CRO management

Cross-disciplinary collaboration

Scientific communication

Independent problem-solving

Education

PhD in Organic Chemistry

Tools

Computational chemistry tools

Job description

About Deep Origin

Deep Origin is a biotechnology company building an operating system for science that transforms how life science research is conducted. Our AI-powered platforms simulate biology, streamline R&D workflows, and enable scientists to model complex biological systems at scale.

As part of strategic government-backed initiatives and the expansion of our AI-driven simulation infrastructure, we are scaling our capabilities in whole-human modeling and predictive toxicology. Exceptional modeling talent is a critical lever in accelerating our mission to reduce disease and extend human health span.

About the Role

We are seeking a Principal/AD Medicinal Chemist to lead and advance small molecule drug discovery programs from early hit identification through IND-enabling studies. This is a senior, hands-on scientific leadership role requiring deep expertise in medicinal chemistry, strategic thinking, and cross-functional collaboration. The candidate will direct work to be completed at a CRO.

This position calls for a highly creative and experienced chemist who can independently design and execute medicinal chemistry strategies while contributing to the integration of computational and AI-driven approaches into drug discovery workflows. The ideal candidate will combine strong technical depth with the ability to guide internal teams and external partners toward impactful outcomes.

Applicants must be authorized to work for any employer in the U.S. We are unable to sponsor or take over sponsorship of an employment Visa at this time.

• PhD in Organic Chemistry or a related field with 3-8 years of industry experience in medicinal chemistry
• Proven track record of advancing drug discovery programs through key milestones (Hit-to-Lead and Lead Optimization)
• Deep expertise in synthetic organic chemistry, including modern methods and reaction mechanisms
• Strong experience in structure-based and ligand-based drug design
• Demonstrated ability to optimize compounds for potency, selectivity, and DMPK/safety properties
• High level of creativity, productivity, and independent problem-solving ability
• Experience managing external CROs and collaborating across disciplines
• Excellent communication skills with the ability to clearly present complex scientific concepts

Nice-to-Have

• Experience working on small molecule degraders, proximity-inducing chemistry
• Experience integrating computational chemistry, machine learning, or AI-driven design into medicinal chemistry workflows
• Background in predictive toxicology or ADMET modeling
• Prior experience contributing to IND-enabling studies or clinical candidate selection
• Familiarity with modern data science tools and cheminformatics platforms

Key Responsibilities

• Propose and independently drive medicinal chemistry strategies to progress programs from hit identification through lead optimization to development candidate selection
• Lead chemistry efforts within cross-functional project teams, which include bench biologists, DMPK lead, non-clinical tox lead, computational scientists, ML engineers
• Design, prioritize, and guide synthesis of novel compounds using structure-based and ligand-based approaches to optimize potency, selectivity, pharmacokinetics and developability
• Interpret and integrate SAR, structural biology, DMPK, pharmacology, and safety data to drive compound design and progression
• Contribute to and integrate AI-driven and computational modeling insights into compound design strategies
• Serve as a technical leader and mentor for internal chemists and external collaborators
• Manage external CRO partnerships to ensure high-quality and timely delivery of chemistry objectives
• Communicate program strategy, data, risks, and recommendations to senior leadership
• Author and contribute to patent strategies and applications, scientific publications, and internal reports

• Competitive compensation aligned with market benchmarks
• Equity participation reflecting long-term impact
• Remote-friendly culture across Europe and the U.S
• Flexible working structure with cross-time-zone collaboration

Values & Cultural Alignment

• Operates with ownership and urgency in ambiguous scientific environments
• Communicates complex modeling concepts with clarity and precision
• Thrives in cross-disciplinary collaboration between science and engineering
• Approaches scientific challenges with intellectual rigor and curiosity
• Balances research depth with practical execution toward milestone delivery

Why This Role Matters Now

Deep Origin is at a pivotal moment in scaling its AI-driven platform to transform drug discovery. As we expand into whole-human modeling and predictive toxicology, medicinal chemistry plays a critical role in translating computational insights into real-world therapeutic candidates.

This role sits at the intersection of cutting-edge AI and traditional drug discovery, offering the opportunity to redefine how medicines are designed—faster, more efficiently, and with greater precision than ever before.