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

Eli Lilly and Company; Indianapolis (IN); On-site; USD 149,000 - 257,000; Full time

Job summary

Eli Lilly and Company is seeking a Senior Research Scientist with a strong background in macrocyclic chemistry to join Early Molecule Design (EMD) in Indianapolis, Indiana. You will lead hit-finding and hit-to-lead efforts for a synthetic macrocycle platform, leveraging SAR and ADME/DMPK expertise to advance orally bioavailable compounds.

The role spans collaboration across multinational teams, guiding design strategies, documenting findings, and mentoring junior scientists.

Qualifications

• Ph.D. in Medicinal Chemistry, Organic Chemistry, Peptide chemistry, or a related field.
• Minimum of 8 years of relevant industry experience in drug discovery.
• Hands-on macrocycle hit-finding and design/synthesis experience.
• Strong ADME/DMPK knowledge and PK/PD relationships.
• Track record of publications or patents.

Responsibilities

• Serve as SME in macrocyclic small molecules/peptides; drive hit-finding strategy and deliver hits.
• Design and synthesize macrocyclic compounds for hit-to-lead progression.
• Apply SAR to drive iterative DMTA cycles balancing potency and drug-like properties.
• Collaborate with Biology, DMPK, and Computational Chemistry to develop design strategies.
• Apply ADME/DMPK principles to optimize oral bioavailability and metabolic stability.
• Contribute to program strategy discussions and go/no-go decisions.
• Communicate findings to internal stakeholders at all levels.
• Maintain ELN documentation in compliance with IP/regulatory requirements.
• Mentor junior scientists and foster collaborative culture.

Skills

Macrocycle hit-finding

Macrocycle design

ADME/DMPK principles

Medicinal chemistry

Cross-functional collaboration

Education

Ph.D. in Medicinal Chemistry/Organic Chemistry/Peptide chemistry/Chemical Biology

Tools

ELN

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.

About The Role

Eli Lilly and Company is seeking an experienced and innovative senior research scientist with strong background in synthetic macrocycles to join Early Molecule Design (EMD) within Lilly Small Molecule Discovery (LSMD) at Indianapolis, Indiana. This individual will drive hit-finding and hit-to-lead chemistry for Lilly’s synthetic macrocycle platform, applying deep expertise in macrocycle design and ADME/DMPK to advance orally bioavailable synthetic macrocycles against challenging targets across Cardiometabolic & Renal (CMR), Immunology, Neuroscience, and Oncology.

The Early Molecule Discovery team's mission is to identify Hits and deliver optimized Leads that advance into strong drug candidates and, ultimately, breakthrough medicines. We are searching for scientific experts recognized for excellence in Hit identification, Lead discovery, and medicinal chemistry to drive the advancement of our portfolio. The EMD team operates as an integrated, multi-site organization spanning Indianapolis, San Diego, Louisville (CO), 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

• Serve as a recognized subject matter expert in macrocyclic small molecules and/or macrocyclic peptides. Drive hit-finding strategy and deliver high-quality, chemically tractable macrocycle hits against novel and challenging targets.
• Design and synthesize macrocyclic small molecules and macrocyclic peptides enabling hit-to-lead progression across multiple therapeutic areas.
• Apply structure-activity relationship (SAR) knowledge to drive iterative DMTA cycles, balancing potency, selectivity, and drug-like properties
• Collaborate closely with Biology, DMPK, Computational Chemistry, and other cross-functional partners to develop and execute efficient molecule design strategies
• Leverage ADME/DMPK principles to optimize oral bioavailability, metabolic stability, permeability, and pharmacokinetic profiles of synthetic macrocycles
• Contribute to program strategy discussions, including target product profile (TPP) development and go/no-go decision frameworks
• 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
• Mentor junior scientists and contribute to a collaborative, scientifically rigorous team culture

Basic Qualifications

• Ph.D. in Medicinal Chemistry, Organic Chemistry, Peptide chemistry, Chemical Biology, or a related field
• Minimum of 8 years of relevant industry experience in drug discovery

Preferred Qualifications

• Demonstrated hands-on experience in macrocycle hit-finding and 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 macrocyclic small molecules
• Experience with challenging or undrugged targets requiring non-traditional modality approaches
• Understanding of clinical translation considerations, including candidate nomination criteria and IND-enabling studies
• Strong scientific publication or patent record
• 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

$148,500 - $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.

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