Advisor, Physicochemical Properties and Compound Quality

Eli Lilly and Company; Indianapolis (IN); On-site; USD 120,000 - 180,000; Full time

Job summary

Eli Lilly and Company in Indianapolis is seeking a highly motivated Analytical Chemist with deep expertise in LC-MS, SFC-MS, and physicochemical analysis to support discovery programs. In this embedded role you will collaborate with medicinal chemists, ADME/DMPK scientists, and data scientists to interpret data, guide synthetic strategy, and advance lead candidates.

You will ensure rigorous documentation and contribute to a world-class compound collection as part of the Discovery Chemistry

Qualifications

• PhD in Analytical Chemistry or Master’s with extensive post-education LC-MS/SFC-MS experience.
• Track record in determining physicochemical properties for drug discovery.
• Experience collaborating with ADME/DMPK and data scientists.

Responsibilities

• Characterize physicochemical properties (solubility, pKa, logD, stability) for NCEs.
• Develop and optimize LC-MS/SFC-MS methods for purity, identity and stability.
• Analyze and interpret complex chromatographic data for project teams.
• Maintain thorough notebooks and compliant documentation of experiments.
• Collaborate with chemists and data scientists to support SAR and lead optimization.

Skills

Analytical chemistry

LC-MS data interpretation

SFC-MS techniques

Data integration

Communication skills

Education

PhD in Analytical Chemistry

Master's in Analytical Chemistry

Tools

LC-MS

SFC-MS

LC-MS/MS

Mass spectrometry instruments

Job description

The Lilly Small Molecule Discovery (LSMD) group is an organization purpose-built to create molecules that make life better for people. We focus on using innovative science to unlock novel approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem-solving through open collaboration and individual accountability.

Advanced Molecule Design (AMD) is dedicated to optimizing molecules into strong drug candidates that become breakthrough medicines for patients. AMD brings together core functional areas — medicinal chemistry, synthetic chemistry, analytical chemistry, computational chemistry, and molecular pharmacology — to accelerate the identification and advancement of high-quality small molecule candidates across a breadth of modalities and therapeutic areas.

Discovery Chemistry Technologies (DCT), a key function within AMD, provides critical scientific expertise and technology solutions that support molecule optimization and scale-up efforts. Within DCT, the Discovery Analytical Chemistry team integrates deep expertise in analytical characterization, separation science, method development, and molecular property assessment to drive compound progression and inform critical portfolio decisions. The team generates high-quality data — spanning structural confirmation, purity determination, stability evaluation, and physicochemical profiling — that enables discovery teams to make rapid, confident decisions across the design-make-test-analyze cycle. Team members are expected to embrace collaboration, adopt a forward-thinking and growth-oriented mindset, and take individual responsibility for their scientific contributions and professional development.

Join our Lilly Small Molecule Discovery team to drive the characterization and optimization of novel drug candidates that could become tomorrow's breakthrough therapies. We're seeking a highly motivated Analytical Chemist with deep expertise in physicochemical property analysis, Liquid Chromatography-Mass Spectrometry (LC-MS), and Supercritical Fluid Chromatography-Mass Spectrometry (SFC-MS) to serve as an embedded analytical expert within our discovery programs.

In this role, you will work directly with medicinal chemists to provide critical analytical insights that guide synthetic strategy and compound progression decisions. Your expertise in ADME/DMPK property profiling, solubility assessment, stability analysis, and structural characterization using LC-MS, SFC-MS, LC-MS/MS, and high-resolution mass spectrometry will be essential to identifying and advancing the most promising lead candidates.

The compounds you characterize and optimize today may become the breakthrough therapies patients need tomorrow. Your analytical insights will directly influence which molecules advance from discovery into clinical development.

You will also lead the integration of purity and stability analyses with our global sample management organization to maintain our world class compound collection

Key Responsibilities:

• Physicochemical Property Characterization:
• Design and execute experiments to measure key physicochemical properties (e.g., solubility, pKa, logD/P, stability, Polar Surface Area) of new chemical entities (NCEs) and drug candidates in the early stages of discovery. These are either measured directly or via surrogate chromatographic methodology, such as SFC-MS or LC-MS. Holistic assessment of these properties in conjunction with other characterization data will guide decisions on SAR, bioavailability, future formulation, and drug delivery.
• LC-MS Method Development & Application Assessing Critical Quality Attributes:
• Develop and optimize LC-MS methods for purity, identity, and stability analysis for a variety of pharmaceutical compounds, impurities, and potential drug candidates. Ensure method sensitivity, reproducibility, robustness, and speed of analytical methods to support the discovery timelines.
• Data Analysis & Reporting:
• Process and interpret complex chromatographic and spectrometric data to generate contextualized and actionable results. Present results and conclusions to cross-functional project teams and key stakeholders to enable rapid and reliable decision making.
• Documentation & Compliance:
• Maintain accurate and detailed laboratory notebooks and reports in accordance with internal company standards. Ensure proper documentation of experimental protocols, results, and any deviations or issues.
• Stay current with advancements in analytical chemistry, LC-MS techniques, and drug discovery trends. Continuously identify opportunities to enhance laboratory efficiency, improve analytical techniques, and contribute to the scientific knowledge base. Demonstrate scientific rigor to develop new and novel experiments and techniques to enable and speed up the discovery pipeline.
• Cross-Functional:

Effectively partner with chemists, pharmaceutical formulation scientists, ADME/DMPK scientists, computational scientists, and data scientists.

Qualifications:

• Minimum:
• PhD in Analytical Chemistry, Pharmaceutical Sciences, or a closely related discipline with 5+ or Masters with 10+ years of post-education hands-on experience with LC-MS, SFC-MS, LC-MS/MS, and physicochemical techniques in a small molecule pharmaceutical discovery environment.
• Preferred
• In-depth proven track record determining physicochemical properties and driving cross-functional impact on drug design and development.
• Experience working closely with ADME/DMPK and providing contextualized results taken from analytical data in early drug discovery.
• Well versed in analytical data/results management.
• Extensive hand-on experience with nominal mass and high resolution LC-MS and SFC-MS instrumentation, including method development, optimization, and troubleshooting (Agilent, Waters, Shimadzu.)
• Expert in the broad range physicochemical properties and their relationship to critical success factors for medicinal chemistry projects
• Deep understanding of chromatography and mass spectrometry theory and proven track record for creatively applying these to the laboratory environment
• Well versed in ADME/DMPK testing strategies and the role of physicochemical properties in early-stage drug discovery.
• Proficiency with data analysis software such as MassLynx, ChemStation, Mestrelabs or similar.
• Demonstrated ability to apply data/information/results workflow enablers such as KNIME and state of the art AI tools.
• Strong analytical and problem-solving abilities.
• Excellent communication skills to effectively present data to both scientific and non-scientific stakeholders.
• Ability to work independently while collaborating effectively with multidisciplinary teams.
• High attention to detail and organizational skills to manage multiple projects simultaneously.
• High learning ability and adaptability.
• Ability to challenge status quo and to influence across organizations.