Director/Sr. Director, Medicinal Chemistry

Job Description

Job Description

Description:

Location: Palo Alto, CA

About GondolaBio  

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. 

Who You Are  

You are a seasoned medicinal chemistry leader with deep, hands-on experience designing and delivering small molecule clinical candidates — not just supporting programs from the sidelines. You have personally led or directly driven lead optimization campaigns from hit-to-lead through candidate nomination, with hands-on experience shaping SAR, guiding synthetic strategy, and making the structural calls that move a program forward. You think in terms of program advancement: what does the data tell us about potency, selectivity, and developability, where are the gaps, and how do we close them rigorously and efficiently. You are as comfortable at the bench or reviewing a synthetic route as you are debating a DMPK tradeoff or a crystal structure with your biology and computational chemistry partners. You set scientific direction, influence program strategy, and communicate complex chemistry rationale clearly to cross-functional partners and governance forums. 

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. Led or been a primary driver of hit-to-lead and lead optimization campaigns, including target selection, SAR analysis, and structure-based drug design 

• Hands-on experience integrating potency, selectivity, ADME/PK, and safety data to guide compound design and candidate selection 
• Deep familiarity with rare disease or genetically defined small molecule targets as a strong differentiator 
• Experience managing CRO and CDMO partners on synthesis, scale-up, and analytical support (nice-to-have, not required) 

Key Responsibilities  

Lead Optimization & Candidate Selection  

• 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 

Synthetic Strategy & Route Development  

• 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 

IND-Enabling Program Support  

• 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 

CRO & External Partner Oversight  

• 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 

Cross-Functional Collaboration & Decision Support  

• 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 

Requirements:

Preferred Education & Experience  

• 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 
• Experience in multiple therapeutic areas preferred 
• 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 

No matter your role at GondolaBio, successful team members are  

• Patient Champions, who put patients first and uphold strict ethical standards. 
• Entrepreneurial Operators, who drive toward practical solutions and have an ownership mindset. 
• Truth Seekers, who are detailed, rational, and humble problem solvers. 
• Individuals Who Inspire Excellence in themselves and those around them. 
• High-quality executors, who execute against goals and milestones with quality, precision, and speed. 

What We Offer  

• Patient Days, where we are fortunate to hear directly from individuals living with the conditions we are seeking to impact throughout the year and learn how we can improve our efforts. 
• A culture inspired by our values: put patients first, think independently, be radically transparent, every minute counts, and let the science speak. 
• An unyielding commitment to always putting patients first. 
• A de-centralized model that enables our program teams to focus on advancing science and helping patients. Our affiliate structure is designed to eliminate bureaucracy and put decision-making power in the hands of those closest to the science. 
• A place where you own the vision – both for your program and your own career path. 
• A collaborative, fast-paced, data-driven environment where we inspire ourselves and each other to always perform at the top of our game. 
• Access to learning and development resources to help you get in the best professional shape of your life. 
• Robust and market-competitive compensation & benefits package (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. 

The base pay range for this position for the United States is $230,000 to $300,000 per year. The actual compensation offered will be determined based on a number of job-related factors, including experience, skills, qualifications, and location. A bonus plan and equity will also be offered.  

GondolaBio ServiceCo is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran or disability status. Employees of BridgeBio and all affiliated companies should work through their managers to inquire about and learn more about this role.