Director/Sr. Director - Medicinal Chemistry (synthetic macrocycles)

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. 

Director/Senior Director, Medicinal Chemistry

Location: Indianapolis, Indiana; San Francisco, CA  |  Function: Macrocycle Chemistry, Advanced Molecule Design (AMD)

Eli Lilly and Company is seeking an experienced and innovative Director/Senior Director with a 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.

• 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

• 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

• 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