Director, Medicinal Chemistry

About the Role

Lilly's Early Molecule Discovery team drives small-molecule hit identification and hit-to-lead progression through structure-based, mechanism-informed, and data-driven design. We are seeking a hands-on medicinal chemistry leader with direct experience advancing molecular glue programs, from hit finding through candidate selection. The role requires close collaboration across pharmacology, structural biology, computational chemistry, and DMPK to translate mechanistic hypotheses into optimized molecules. Success requires both deep bench-level chemistry expertise and the interpersonal and cross-functional leadership skills to guide internal and external teams.

Responsibilities

• Lead hit-to-lead optimization of screening hits, improving potency, selectivity, physicochemical properties, and ADMET.
• Apply structure-based and data-driven design, incorporating ternary complex structural data where relevant.
• Design and synthesize novel molecules to test mechanistic hypotheses, including cooperativity-driven SAR for molecular glue chemotypes.
• Design and implement screening cascades tailored to molecular glue pharmacology.
• Direct internal and external medicinal chemistry resources, including CRO relationships, to keep programs aligned with strategy and timelines.
• Oversee high-throughput synthesis, route scouting, and scale-up to enable efficient compound delivery.
• Maintain a strong safety culture and efficient lab operations.

Basic Qualifications

• PhD in Organic Chemistry or related Chemistry field with 8+ years of relevant experience in small molecule drug discovery; MS with 10+ years; or BS with 12+ years.

Preferred Skills and Experience

• Extensive experience in medicinal chemistry, SAR analysis, and structure- and mechanism-based molecular design.
• Direct experience designing or optimizing molecular glue degraders, including protein–protein interface engagement, E3 ligase biology, and neosubstrate identification.
• Demonstrated leadership as a chemistry lead on programs of any mechanism—ideally including a molecular glue program—that reached candidate selection.
• Track record of scientific contributions through publications, patents, or external presentations.
• Experience managing or collaborating with external chemistry teams and CROs.
• Experience with novel modalities, such as targeted protein degradation and covalent chemistry, and biophysical techniques to mechanistically understand molecular glue SAR.
• Familiarity with computational drug design tools (e.g., LiveDesign, MOE, Maestro) and AI-enabled chemistry tools.
• Self-driven, with a growth mindset and adaptability to fast-evolving science.
• Strong communication and collaboration skills in multidisciplinary, matrixed environments.

Pay

Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is $163,500 - $257,400. Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

Benefits

• Company-sponsored 401(k)
• Pension
• Vacation benefits
• Medical, dental, vision and prescription drug benefits
• Flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts)
• Life insurance and death benefits
• Time off and leave of absence benefits
• Well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)