Scientific Director — Synthetic Process Chemistry (Peptides & Small Molecules)

Eli Lilly and Company • Indianapolis, IN

23h • $148,500 - $257,400 • Onsite

About The Position

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. Join the process chemistry team behind Mounjaro® and Zepbound® — two of the most impactful medicines in the world — and help shape the next generation of breakthroughs, including retatrutide, Lilly’s first-in-class GIP/GLP-1/glucagon triagonist. An exciting opportunity is available for a highly skilled and experienced scientist with expertise in synthetic process chemistry to join SMDD at Eli Lilly and Company. You will be part of a dynamic, cross-functional department supporting one of the most productive peptide portfolios in the industry, spanning Discovery through Commercial phase, at the forefront of sustainable peptide development and commercialization. Our core commercial strategy centers 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 consurtium. 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. Critically, this is a hands-on scientific role — the successful candidate will be expected to work at the bench alongside their team, not only direct from the sidelines. 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.

Requirements

• Ph.D. in Chemistry or a closely related field with 7+ years of pharmaceutical industry experience in peptide or synthetic process chemistry; or M.S. with 10+ 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.
• Experience with tech transfer of processes into manufacturing operations, including CMOs.
• 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.

Nice To Haves

• 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.
• Knowledge and experience with management of technical projects across multiple programs.
• 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.
• Demonstrated leadership capabilities, especially in cross-functional team environments.
• Ability to prioritize multiple activities and influence others to promote a positive work environment.

Responsibilities

• Serve as a hands-on scientific leader — personally conducting bench-level LPPS and condensation chemistry development while 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 Phase 1 and 2 (and potentially Phase 3) 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.

Benefits

• company bonus (depending, in part, on company and individual performance)
• company-sponsored 401(k)
• pension
• vacation benefits
• 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
• well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level