Director, Medicinal Chemistry

100 Eli Lilly and Company; United States; On-site; USD 164,000 - 257,000; Full time

Benefits offered by this job

Health benefits

Dental benefits

Vision benefits

401(k) plan

Bonus program

Job summary

Lilly's Early Molecule Discovery team is seeking a hands-on medicinal chemistry leader to advance molecular glue programs from hit finding through candidate selection. The role requires collaboration across pharmacology, structural biology, computational chemistry, and DMPK to translate mechanistic hypotheses into optimized molecules, with leadership of internal and CRO teams.

Ideal candidates will have deep bench chemistry expertise, strong cross-functional communication, and a track record in

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.
• 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.

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.

Skills

Medicinal chemistry

SAR analysis

Structure-based design

Molecular glue design

Leadership

Education

PhD in Organic Chemistry

MS in Chemistry

BS in Chemistry

Tools

LiveDesign

MOE

Maestro

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

Overview

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.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status. Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women's Initiative for Leading at Lilly (WILL).

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).

In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for 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; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).

Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly's compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

Company Culture

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly