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

Job ID: R-106626Company: LillyLocation: Indianapolis, Indiana, United States of AmericaJob Type: Full TimeCategory: Research & DevelopmentPosted Date: 2026-06-01At 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 around the world 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 give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.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.Top candidates for this position will be expected to: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.Basic Qualifications: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. The position level is flexible and will be commensurate with the successful candidate’s experience — we welcome applications from early mid-career scientists through senior leaders with an established track record.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.Additional Preferences: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.Additional Information:Position Location: Indianapolis, INThe physical demands of this job are consistent with a laboratory environment.Travel: 0 to 10% (domestic and international, including CMO and conference travel)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 () 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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is$148,500 - $257,400Full-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.#WeAreLillySkillssynthetic process chemistryliquid phase peptide synthesispeptide synthesistech transfergreen chemistryprocess mass intensitycontinuous flow chemistryproject managementcross-functional leadershipcommunication skillsmentoringcollaborationanalytical skills