Scientific Director, Process Chemistry - Oligonucleotides

Eli Lilly and Company; Indianapolis (IN); On-site; USD 148,500 - 257,400; Full time

Benefits offered by this job

Company-sponsored 401(k)

Comprehensive medical benefits

Flexible spending accounts

Job summary

Initial Therapeutics, Inc. is seeking a skilled scientist for their Synthetic Molecule Design and Development team in Indianapolis, IN. This role requires extensive expertise in oligonucleotide CMC, focusing on the development and optimization of synthetic drug processes. Qualified candidates must hold a PhD or MS and possess several years of industry experience. Responsibilities include leading CMC activities for clinical trials, developing impurity control strategies, and collaborating with internal and external partners. Competitive compensation package offered including health benefits.

Qualifications

• 5+ years of relevant industry experience in synthesis, oligonucleotides, and CMC.
• Experience in pharmaceutical sector active ingredient development.
• Tech transfer experience into manufacturing operations.

Responsibilities

• Lead CMC activities to support clinical trials and regulatory submissions.
• Develop and apply impurity control strategies.
• Provide technical leadership for process scale-up.

Skills

Oligonucleotide CMC expertise

Synthesis

Solid-phase synthesis

Process development

Regulatory interactions

Education

PhD in a relevant scientific discipline

MS in a relevant scientific discipline

Job description

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 and Position 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.

Our SMDD team is looking for experienced and creative candidates with experience in chemistry, manufacturing, and controls (CMC) of oligonucleotides to participate in the development of chemistry in support of scalable and environmentally friendly manufacturing processes. This technical role will support emerging synthetic needs across the rapidly evolving Lilly Genetic Medicines (LGM) portfolio. The scientist will collaborate with a growing team comprising chemists, analysts, and engineers focused on the development and optimization of existing methods and exploration of novel synthetic approaches to oligonucleotides and their conjugates. The position presents an opportunity to lead CMC activities to support clinical trials, product commercialization, and regulatory submissions of oligonucleotide therapeutics. Developing and working with both internal manufacturing (Lilly Medicine Foundry) and external contract manufacturing organizations (CMOs) to support oligonucleotide synthesis, tech transfer, and campaign execution will be important aspects of this role.

Responsibilities

• Bring extensive oligonucleotide CMC expertise to SMDD and grow internal capability through coaching, mentorship, and technical leadership across a diverse portfolio — complex single strands, siRNA, and oligonucleotide conjugates (AOC and PRC).
• Apply modern synthetic organic and nucleic acid chemistry to challenge existing methods, define new manufacturing technologies, and address key CMC challenges across the LGM portfolio.
• Develop and apply impurity control strategies aligned with the current global regulatory climate; address CMC regulatory questions enabling clinical studies and marketing authorization applications. Prior experience in validation activities preferred.
• Provide technical leadership across route design, process development, equipment selection, and scale‑up — from laboratory plans through demonstration on development- and commercial‑scale equipment, partnering with internal manufacturing (Lilly Medicine Foundry) and external CMOs to deliver robust processes for clinical and commercial supply.
• Demonstrate strong skills with automated reactor platforms and purification technologies and apply them across the oligonucleotide portfolio.
• Collaborate across internal CMC networks (Drug Product Delivery, Project Management, Quality, Manufacturing, and Regulatory) to deliver materials and documentation for clinical trials and regulatory submissions.
• Identify and integrate external chemistry innovations to complement internal capabilities; represent Lilly externally through presentations at symposia and consortia and publications in peer‑reviewed journals.
• Contribute novel chemical design and mechanism‑based problem solving (e.g., total synthesis, methodology development, oligonucleotide synthesis), reflected in a strong peer‑reviewed publication record.
• Lead through ambiguity and change; encourage initiative, accountability, and diverse perspectives across the team.

Basic Qualifications

• PhD in a relevant scientific discipline with 5+ years of relevant industry experience (synthesis, oligonucleotides, solid‑phase synthesis, CMC); or
• MS in a relevant scientific discipline with 8+ years of relevant industry experience (synthesis, oligonucleotides, solid‑phase synthesis, CMC).
• Experience within the pharmaceutical sector: active ingredient development and associated formulated products; developing chemical processes from mid‑development (proof of concept) through commercialization.
• Experience in development and CMC including quality and regulatory interactions.
• Experience with tech transfer of processes into manufacturing operations.

Additional Preferences

• Strong interpersonal skills and a collaborative working style.
• Demonstrated initiative and appropriate risk‑taking.
• Demonstrated technical proficiency and ability to create ideas for future work plans.
• Strong technical skills that deliver business value.
• Knowledge and experience with management of a technical project.
• Demonstrated leadership capabilities, especially in a team environment.
• Ability to prioritize multiple activities and manage ambiguity.
• Ability to influence others to promote a positive work environment.
• Demonstrated success in persuasion, influence, and negotiation.

Physical Demands/Travel

• Position Local: Indianapolis, IN; Lilly Technology Center‑North (LTC‑N)
• The physical demands of this job are consistent with a lab environment.
• Travel: 0 to 10%

Work Environment

This position’s work environment is in a laboratory environment.

Accommodation and EEO

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.

Compensation and Benefits

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 will also 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.