Principal Scientist, Computational Chemistry

About the role

Eikon Therapeutics is a biopharmaceutical company focusing on discovering novel treatments for life-threatening diseases using advanced technology at the intersection of chemistry, engineering, computation, and biology. Our discovery platform leverages groundbreaking innovations from our founders (Nobel Prize, 2014) to develop microscopes capable of real-time, molecular-resolution measurements of protein movement in living cells, thus opening up previously inaccessible protein classes as drug targets.

Position

We are seeking a Principal Scientist in Computational Chemistry with a proven track record of applying in silico technologies to identify high-quality lead-like molecules against challenging therapeutic targets. The ideal candidate will utilize AI/ML to enhance library design, hit identification, virtual screening, and hit-to-lead efforts across various projects. This role requires expertise in protein modeling, AI-assisted structure/affinity predictions, binding site assessment, homology-based chemistry mining, virtual screening, and compound procurement. Collaboration with biologists, medicinal chemists, software engineers, and machine learning experts is essential.

About You

You are a computational chemistry/cheminformatics expert with a passion for drug discovery and a strong background in solving complex problems. You are collaborative, resourceful, open-minded, data-driven, and able to operate with urgency. You thrive in a fast-paced, dynamic environment and enjoy pushing technological boundaries to find innovative solutions.

What You’ll Do

• Deliver virtual screening workflows that incorporate physics- and AI-based modeling methods, including ligand- and structure-based techniques, ensemble docking, molecular dynamics, and free energy calculations
• Support computational chemistry across our drug discovery pipeline, covering target selection, HTS, hit identification/calling, hit-to-lead, and lead optimization
• Provide guidance on modern cheminformatics and ML/AI methods for library design (diversity, focused, fragment, DEL) and data analysis from HTS campaigns to build predictive models
• Routinely analyze and interpret structural and physicochemical properties to inform synthetic strategies
• Collaborate with medicinal chemists to prioritize emerging hits for synthesis and purchase
• Work with our data science team to integrate advanced AI/ML tools into our chemistry and drug discovery processes

Qualifications

• PhD in Computational Chemistry or related field with 10+ years of relevant experience; or Master's with 18+ years; or Bachelor's with 20+ years
• Expertise in virtual screening, HTS triaging, hit calling, and diversity analysis
• Proficiency in computational chemistry software like Schrödinger Suite, Rosetta, AlphaFold, Gromacs, or similar tools
• Experience with physics-based methods, molecular dynamics, conformational analysis, free energy perturbation, and quantum mechanics
• Knowledge of cheminformatics data analysis, data mining, and machine learning models for drug discovery
• Experience with ligand-based design approaches, QSAR, QSPR, multiparameter optimization, and rationalizing SAR to design novel molecules
• A publication record, patents, or conference presentations in computational chemistry and/or drug discovery
• Proficiency in scientific programming languages (e.g., Python, KNIME) and data analytics tools (e.g., Spotfire, DataWarrior, Pandas)
• Excellent problem-solving skills and ability to work effectively in a fast-paced, dynamic research environment
• Strong communication skills to convey complex scientific concepts to both technical and non-technical stakeholders

Benefits

• 401(k) plan with company matching
• Medical, dental, and vision insurance with premiums covered by Eikon at 95%, 100%, and 100% respectively
• Mental health and wellness benefits
• Week-long summer and winter holiday shutdowns
• Generous paid time off and holiday policies
• Life/AD&D Insurance with premiums covered by Eikon at 100% and optional supplemental employee-paid life/AD&D policies
• Enhanced parental leave benefit
• Daily subsidized lunch program when on-site

Pay

The expected salary range for this role is $204,000 to $223,250, depending on skills, competency, and market demand for your expertise.