Director/Senior Director, Medicinal ChemistryLocation: Indianapolis, Indiana; San Francisco, CA | Function: Macrocycle Chemistry, Advanced Molecule Design (AMD)
About the RoleEli Lilly and Company is seeking an experienced and innovative Director/Senior Director with strong background in synthetic macrocycles and macrocyclic peptides to join the Advanced Molecule Design (AMD) Medicinal Chemistry organization in Indianapolis, Indiana. This individual will contribute across all four therapeutic areas - Cardiometabolic & Renal (CMR), Immunology, Neuroscience, and Oncology - applying deep expertise in macrocyclic peptide design and small molecule ADME/DMPK to advance high-quality drug candidates into and through development.
The AMD Medicinal Chemistry team operates as an integrated, multi-site organization spanning Indianapolis, San Diego, San Francisco, Louisville, and Alcobendas (Spain). This role offers exposure to a broad and innovative portfolio with meaningful opportunities to shape program strategy, influence molecule quality, and collaborate across a world-class cross-functional organization.
Key Responsibilities- Design and synthesize macrocyclic small molecules and macrocyclic peptides in support of drug discovery programs across multiple therapeutic areas
- Apply structure-activity relationship (SAR) knowledge to drive iterative DMTA cycles, balancing potency, selectivity, and drug-like properties
- Leverage ADME/DMPK principles to optimize oral bioavailability, metabolic stability, permeability, and pharmacokinetic profiles of macrocyclic and peptidic modalities
- Serve as a recognized subject matter expert whose compound design and SAR insights resolve critical scientific challenges and advance programs through key milestones
- Collaborate closely with Biology, DMPK, Computational Chemistry, and other cross-functional partners to develop and execute efficient molecule design strategies
- Contribute to program strategy discussions, including target product profile (TPP) development and go/no-go decision frameworks
- Proactively identify capability gaps in tools, methods, or synthetic approaches, and champion new strategies - including AI/ML-enabled design - that improve cycle times and design quality across the portfolio
- Effectively communicate scientific findings to internal stakeholders at all levels, including program teams, portfolio boards, and leadership
- Maintain thorough and timely documentation in electronic laboratory notebooks (ELN) in accordance with IP and regulatory requirements
- Lead or contribute to continuous improvement initiatives and coaching efforts that strengthen the broader team's scientific rigor and impact
Basic Qualifications- Ph.D. in Medicinal Chemistry, Organic Chemistry, Peptide Chemistry, Chemical Biology, or a related field with a minimum of 8+ years of drug discovery experience in the pharmaceutical or biotechnology industry; or BS/MS with 15+ years equivalent experience
Preferred Qualifications- Demonstrated hands-on experience in the design and synthesis of macrocyclic peptides or macrocyclic small molecules
- Strong foundation in ADME/DMPK principles and their application to drug design, including oral bioavailability, metabolic stability, and PK/PD relationships
- Track record of productive multi-disciplinary collaboration in a pharmaceutical or biotechnology research environment
- Experience across multiple therapeutic areas or modalities, including both macrocyclic peptides and small molecules
- Experience with challenging or undrugged targets requiring non-traditional modality approaches
- Track record of advancing programs to candidate selection
- Track record of publications, patents, or scientific contributions
- Excellent written and oral communication skills; ability to present complex scientific data clearly to diverse audiences
Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$163,500 - $281,600
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.
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