Scientific Director — Incretin & Peptide Process Chemistry

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 153,000 - 264,000; Full time

Benefits offered by this job

401(k) plan

Pension and well-being benefits

Job summary

Lilly’s Synthetic Molecule Design and Development (SMDD) group seeks a senior scientist to lead LPPS and peptide process chemistry, driving greener manufacturing across the portfolio. You will mentor chemists, optimize routes, and collaborate across US, Asia, and Europe to enable scalable production for Mounjaro and Zepbound.

The role emphasizes leadership, cross-functional teamwork, and external publication, with strategic impact from lab discovery to commercial production in the Medicines

Qualifications

• Ph.D. in Chemistry with 7+ years of pharma experience in peptide or synthetic process chemistry.
• Proven leadership of scientists and cross-functional project teams.
• Experience with SPPS, LPPS, and/or hybrid peptide synthesis at scale.
• Strong publication and presentation record in peptide or synthetic chemistry.
• Excellent communication to technical and business audiences.

Responsibilities

• Provide technical direction on LPPS and condensation chemistry and mentor peptide chemists.
• Lead technology development and transfer early-phase processes to Medicines Foundry (Lebanon, Indiana).
• Collaborate with Manufacturing to transfer processes for validation at internal facilities or CMOs.
• Guide CMO partners in greener peptide development and manufacture.
• Engage with Development and Manufacturing to drive continuous improvement in processes.
• Implement greener chemistry and PMI benchmarking across development stages.
• Present findings at internal forums and external conferences; publish in peer‑reviewed journals.
• Communicate technical and business implications to scientific and non‑scientific audiences.

Skills

Leadership

Process chemistry

LPPS/SPPS

Communication

Cross-functional teamwork

Education

Ph.D. in Chemistry

M.S. in Chemistry

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

At Lilly, we serve an extraordinary purpose. We make a difference for people around the globe by discovering, developing and delivering medicines that help them live longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism.

Organization Summary

The Synthetic Molecule Design and Development (SMDD) organization is responsible for the development of synthetic drug substances and drug products from the pre‑clinical phase through commercialization. Our scientists and engineers develop innovative technical solutions to advance an existing portfolio that includes small molecules, synthetic peptides, oligonucleotides, and other emerging therapeutic modalities to help bring the next generation of life-changing medicines to patients. Be part of the process chemistry team behind Mounjaro® and Zepbound® — two of the most impactful incretin medicines in the world — and help shape the next generation of breakthroughs, including retatrutide, Lilly’s first‑in‑class GIP/GLP‑1/glucagon triagonist.

Position Summary

An exciting opportunity is available for a skilled and experienced scientist with expertise in synthetic process chemistry to join SMDD’s incretin and peptide process chemistry team at Eli Lilly and Company. You will be part of a dynamic, cross‑functional department supporting a highly productive peptide portfolio, spanning through Commercial phase, at the forefront of sustainable peptide development and commercialization. Our core commercial strategy centres on traditional Liquid Phase Peptide Synthesis (LPPS) — applying small molecule‑inspired fragment condensation chemistry to manufacture complex peptides like those found in Mounjaro® and Zepbound® at global scale. Sustainability is not an afterthought here — it is a strategic imperative embedded in everything we do, from reducing Process Mass Intensity (PMI) and eliminating hazardous reagents to publishing green chemistry innovations and leading industry‑wide initiatives through the ACS GCI Pharmaceutical Roundtable and IQ consortium. In this role, you will lead peptide commercialization projects built on this proven platform, championing greener process design at every stage. You will work closely with a growing team of chemists, analysts, and engineers to design synthetic routes, optimize condensation chemistry, and set a new standard for responsible peptide manufacturing. This role operates in a highly collaborative environment with key partners across the United States, Asia, and Europe. This is primarily a scientific leadership role, with the expectation that the successful candidate will periodically engage at the bench to guide, troubleshoot, and mentor their team. Technology developed in this role will feed directly into Lilly’s Medicines Foundry, a state‑of‑the‑art manufacturing facility coming online in Lebanon, Indiana within the next two years, giving this position rare end‑to‑end impact from laboratory discovery through commercial production.

Responsibilities

• Serve as a scientific leader — providing technical direction on LPPS and condensation chemistry development, and leading and mentoring a team of peptide chemists across commercial and pipeline programs.
• Lead internal technology development and coordinate the transfer of early‑phase processes to Lilly’s Medicines Foundry (Lebanon, Indiana) — a next‑generation facility supporting Phase1 and 2 (and potentially Phase3) clinical supply.
• For late‑phase programs, collaborate with Lilly’s internal and external Manufacturing groups to transfer processes for validation at internal facilities or external CMO partners.
• Educate and guide CMO partners in best practices for greener peptide development and manufacture.
• Engage with Lilly’s Development and Manufacturing organizations to develop a deep understanding of new initiatives and drive continuous improvement in existing scientific processes.
• Implement green chemistry and engineering solutions across all stages of process development — from solvent selection and reagent optimization to PMI benchmarking and publication of sustainability innovations in peer‑reviewed journals and industry forums.
• Present research findings at internal forums and external conferences; publish in high‑quality, peer‑reviewed journals.
• Communicate technical and business‑related implications of your work effectively to both scientific and non‑scientific audiences.

Basic Qualifications

• Ph.D. in Chemistry with 7+ years of pharmaceutical industry experience in peptide or synthetic process chemistry; or Ph.D. in Chemistry with 15+ years of combined pharmaceutical industry and academia experience; or M.S. with 15+ years of equivalent industry experience.
• Demonstrated leadership in managing scientists and cross‑functional project teams.
• Experience with SPPS, LPPS, and/or hybrid peptide synthesis strategies at scale.
• Track record of external publication and presentation in the peptide or synthetic chemistry field.
• Strong communication skills, including the ability to present to both technical and business audiences.

Additional Preferences

• Experience with tech transfer of processes into manufacturing operations, including CMOs.
• Excellence in multiple modes of peptide synthesis, including hybrid SPPS/LPPS and Tag‑Assisted Liquid Phase Peptide Chemistry (TA‑LPPS).
• Experience with continuous flow chemistry, process intensification, or novel coupling reagent platforms.
• Familiarity with regulatory CMC requirements for peptide drug substances.
• Experience working with global CMO partners in Asia and/or Europe.
• Strong interpersonal skills and a collaborative working style.
• Demonstrated initiative, appropriate risk‑taking and ability to lead through ambiguity.
• Active participation in or awareness of professional societies and industry consortia relevant to pharmaceutical process chemistry and sustainability, including ACS, TIDES, the ACS Green Chemistry Institute Pharmaceutical Roundtable, and the IQ Consortium.

Additional Information - Physical Demands/Travel

Position Location: Indianapolis, IN. The physical demands of this job are consistent with a combined office and laboratory environment. Travel: 0 to 10% (domestic and international, including CMO and conference travel). The physical demands here are representative of those that must be met by an employee to successfully perform the essential functions of this job.

Work Environment

This position’s work environment is a mix of office and laboratory settings. The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job. To perform this job successfully, an individual must be able to perform the role and responsibilities satisfactorily. The requirements listed above are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. 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.

Benefits

• Inclusive, 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).

Employee Resource Groups (ERGs)

• 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)
• Women’s Initiative for Leading at Lilly (WILL)

Compensation

The anticipated wage for this position is $153,000 - $264,000. 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).

#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!