Sr. Director/Executive Director, Computational Chemistry

Prelude Therapeutics Incorporated • Wilmington, DE

3d

About The Position

We are seeking a highly accomplished and hands-on Executive Director of Computational Chemistry to build and lead our computational drug discovery capabilities in a fast-growing biotech environment. This leader will drive the design of novel small molecules against high-value biological targets using structure-based drug design (SBDD), physics-based modeling, and cutting-edge AI/ML approaches.
The successful candidate will directly contribute to active discovery programs while also leading the implementation of AI tools across the discovery organization. The Executive Director will serve as both a scientific driver and a platform builder, partnering closely with Medicinal Chemistry, Biology, Structural Biology, and executive leadership to accelerate pipeline progression.

Requirements

• Ph.D. in Computational Chemistry, Biophysics, Chemical Physics, or related discipline.
• 5–20 years of industry experience supporting small-molecule drug discovery.
• Demonstrated success partnering with medicinal chemistry programs that have advanced into clinical development
• Deep expertise in SBDD, docking, molecular dynamics, FEP, and cheminformatics.
• Strong working knowledge of AI/ML applications in molecular design, generative chemistry, and predictive modeling.
• Hands-on leader who remains scientifically engaged.
• Strong cross-functional collaborator with executive presence.
• Passionate about building AI-enabled drug discovery platforms that deliver transformative therapeutics.

Responsibilities

• Define and execute computational chemistry strategy from target validation through candidate nomination.
• Lead structure-based drug design efforts to enable hit identification and lead optimization.
• Identify, evaluate, and deploy AI tools across medicinal chemistry, biology, DMPK, and translational research.
• Personally contribute to programs using molecular docking, virtual screening, molecular dynamics, and free energy methods (FEP/TI).
• Leverage structural biology data (X-ray, cryo-EM, homology models, AlphaFold) to guide rational design.
• Drive scaffold hopping, de novo design, and multi-parameter optimization strategies.
• Implement generative chemistry, predictive ADME/Tox models, and decision-support systems.
• Promote AI adoption and literacy across the R&D organization.

What This Job Offers

• Job Type: Full-time
• Career Level: Director
• Education Level: Ph.D. or professional degree
• Number of Employees: 11-50 employees