Principal Scientist / Associate Director, Medicinal Chemistry

Job Description

Job DescriptionDescription:

Principal Scientist / Associate Director, Medicinal Chemistry 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

• A highly driven medicinal chemist who owns the chemical strategy for a peptide-based drug discovery program - from design and synthesis to structure-activity relationships and candidate optimization.
• Trained in a top-tier academic lab and/or strong industry setting with a compelling publication record demonstrating scientific rigor and independence.
• Hands-on expertise in peptide medicinal chemistry (e.g., SPPS, peptide stapling/cyclization, peptidomimetic design, multiparameter optimization), with a track record of turning synthetic challenges into decision-grade chemical matter.
• Comfortable partnering tightly with biology, DMPK, and tox to shape the screening cascade, drive SAR, and make hit-to-lead and lead optimization decisions.
• A crisp communicator and pragmatic operator who can lead a chemistry workstream internally and through CROs/academic collaborators with high standards.

KEY RESPONSIBILITIES

• Lead the medicinal chemistry strategy for a peptide drug-discovery program, including synthetic design, SAR hypothesis generation, and translational path to IND-enabling decisions.
• Design, synthesize, and optimize peptide and peptidomimetic compounds with a focus on potency, selectivity, stability, and drug-like properties.
• Build and drive a fit-for-purpose chemistry campaign: analog design, synthetic route development, structure-activity analysis, and multiparameter optimization.
• Own scientific direction and quality for externalized chemistry work (CROs/synthesis partners): study design, protocol review, data review, and clear go/no-go recommendations.
• Communicate complex SAR data clearly in program forums; contribute to IP and publications and help shape program direction with leadership.
• Provide scientific mentorship to junior chemists and hold CROs and partners to rigorous, decision-quality standards.

PREFERRED EDUCATION & EXPERIENCE

• PhD in organic chemistry, medicinal chemistry, chemical biology, or related field (or equivalent experience) with a strong publication record, ideally from a high-caliber lab.
• 8+ years of hands-on industry experience in peptide medicinal chemistry, including SPPS, peptide stapling/cyclization, peptidomimetic design, and multiparameter optimization.
• Experience generating decision-quality chemistry in a discovery setting: SAR analysis, candidate selection, and cross-functional influence in a drug discovery team.
• Proven ability to drive work through CROs/partners and collaborate effectively across biology, DMPK, and translational functions.

NICE-TO-HAVES

• Experience with advanced peptide modalities: stapled peptides, bicyclic peptides, peptide-drug conjugates, or macrocyclic peptidomimetics.
• Familiarity with structural biology or biophysical techniques (X-ray crystallography, NMR, SPR) to guide structure-based design.
• Knowledge of formulation considerations for peptide therapeutics (oral delivery, half-life extension strategies, conjugation chemistry).
• Deep disease-area chemistry knowledge relevant to the program and an understanding of translational biomarker strategy.
• Prior experience in a fast-paced biotech/startup environment where you owned a chemistry workstream end-to-end.

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

COMPENSATION

The base pay range for this position is $185,000 to $215,000 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.

Requirements: