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)

About the Role

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.

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

Why Lilly

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism.

We offer a competitive compensation and benefits package, a collaborative and innovative work environment, and meaningful opportunities for career development and scientific growth within one of the most productive pipelines in the industry.

Lilly is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability, or any other legally protected status.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

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 - $239,800

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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