Director/Sr. Director, Medicinal Chemistry

GondolaBio Service Co • San Francisco, CA

5d • Onsite

About The Position

GondolaBio is a clinical-stage biopharmaceutical company focused on developing breakthrough therapeutics for genetic diseases. GondolaBio is an independent sister company to BridgeBio, originally carved out in 2024 after securing $300M in private financing from external investors. GondolaBio aims to leverage cutting-edge biological research to discover, create, test, and deliver transformative medicines to treat patients who suffer from genetic diseases. We are seeking an experienced and innovative medicinal chemist to join a fast-paced, and multidisciplinary team working on the development of the therapeutics for the disease rooted from genetic mutations. In this role, you will provide medicinal chemistry leadership on small molecule projects. Your in-depth knowledge of medicinal chemistry and proven track record of driving small molecules from hit identification through clinical candidate nomination will be the key to the success of the projects.

Requirements

• PhD in Organic Chemistry or Medicinal Chemistry
• 10-15+ years of pharma/biotech industrial drug discovery experience with a strong track record in leading medicinal chemistry programs from hit-to-lead and lead optimization, drug profiling, and to drug candidate nominations
• Deep expertise in SAR-driven design, structure-based drug design, ADME/PK optimization, and multi-parameter optimization
• A deep understanding of the pharmacology, DMPK, CMC, and toxicology requirements of a strong drug candidate
• Strong experience in optimizing molecular properties, including potency, selectivity, safety profile, and overall developability of small molecule series
• Deep expertise in synthetic organic chemistry, retrosynthesis, route design, and practical execution of complex multistep syntheses.
• Experience directing CRO-based chemistry programs; proven vendor oversight and delivery management
• Effective written and verbal communication skills, with the ability to present findings clearly and concisely.
• Ability to work collaboratively in a team environment.
• High level of scientific rigor, accuracy and attention to detail in all aspects of work.

Nice To Haves

• Direct experience with rare disease or genetically defined targets
• Experience with computational or structure-based design platforms (e.g., FEP, docking, crystallography-driven design)
• Exposure to process chemistry, CMC, or scale-up considerations
• Prior experience in a small or fast-growing biotech environment
• Experience managing CRO and CDMO partners on synthesis, scale-up, and analytical support

Responsibilities

• Responsible for the design and execution of efficient medicinal chemistry strategies that drive the drug discovery process – including hit and lead identification, lead optimization, ADME/PK, pharmacology, and toxicology - to successfully deliver development candidates
• Develop expeditious structure-activity-relationship (SAR) through iterative design-make-test cycles. Utilize SAR-driven design, structure-based drug design, computational/ML/AI tools, and multi-parameter optimization approach to optimize potency, selectivity, physicochemical properties, ADME/PK properties, and safety profiles
• Strategically select compounds for advancement to ADMET, PK, physiochemical property assays, and in vivo pharmacology evaluations to identify high quality drug candidates
• Guide synthetic route design and process feasibility assessment from discovery through candidate nomination
• Partner with process chemistry and CMC teams to ensure early synthetic routes translate into scalable, developable processes
• Identify technical risks in synthesis or scale-up and recommend mitigation strategies ahead of IND-enabling work
• Contribute directly to IND-enabling chemistry deliverables, including compound supply strategy, analytical characterization, and impurity/degradant assessment
• Serve as a senior scientific leader on small molecule programs, providing expert review of chemical design strategies and structure-activity rationale
• Critically evaluate complex chemistry and biology datasets and synthesize data-driven recommendations for program decisions
• Provide scientific oversight of CRO- and CDMO-executed work — synthesis, analytical characterization, and scale-up — including study design input, protocol review, data package review, and final reports
• Serve as primary scientific point of contact with external partners to ensure scientific rigor, clear communication, and timely delivery
• Maintain broad awareness of latest technologies, external platforms, competitive landscape, and assets of interest and participate in diligence efforts to evaluate and provide recommendations on these opportunities
• Collaborate closely with biology, DMPK, toxicology, translational, and clinical teams to support data-driven program decisions
• Summarize data in presentations, technical reports, and team discussions to support decision-making
• Clearly communicate complex chemistry datasets and program rationale in team meetings and governance forums

Benefits

• Base, Performance Bonus, Equity, health, welfare & retirement programs
• Flexible PTO
• Rapid career advancement for strong performers
• Potential ability to work on multiple GondolaBio Pharma programs across multiple therapeutic areas over time.
• Partnerships with leading institutions.
• Commitment to Diversity, Equity & Inclusion.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree