Associate Director, Computational Chemistry

Location: Newark, CA
Job : 401
# of Openings: 0

Protagonist Therapeutics is seeking a talented and highly motivated computational chemist to join our Drug Design group. The successful candidate will leverage proprietary molecular modeling tools, commercial software packages, and AI algorithms to design novel compounds and optimize existing leads. Protagonist is advancing the development of orally stable peptides, peptidomimetics, and small molecules. The ideal candidate will hold a PhD in computational chemistry, bioinformatics, artificial intelligence, or a related discipline and will have broad hands‑on experience across all aspects of molecular design that directly impact IND candidate selection.

In addition, the candidate must be well versed in molecular recognition, structure‑activity relationship (SAR) development, and potency optimization. Strong familiarity with public‑domain sequence, functional, and structural databases, along with extensive scripting and programming expertise, is required. Knowledge of AI‑driven drug design is highly desirable. The ideal candidate will also possess significant expertise in constrained peptides, macrocycles, peptide engineering, and small‑molecule design.

The candidate must be well versed in the relevant scientific literature and demonstrate proven hands‑on experience in structure‑based drug design within an industrial setting.

• Leading structure-based and/or ligand-based drug design for one or more targets
• Maintaining up-to-date knowledge of the scientific literature relevant to assigned targets
• Optimizing the binding affinity of peptide derivatives while simultaneously enhancing their oral stability and pharmacokinetic properties
• Utilizing computational drug-design tools (such as database searching, molecular docking, molecular dynamics (MD) simulations, and scoring functions) to design biologically active molecules
• Interpreting and integrating structural, biological assay, stability, mutagenesis, sequencing, and pharmacological data to guide the design of biologically active compounds

• PhD in computational chemistry or a closely related discipline
• Proven translational experience advancing projects toward IND candidates
• In-depth knowledge of constrained peptides, peptidomimetics, and macrocycles
• Practical experience optimizing the stability of peptides and/or macrocycles
• Proficiency in writing scripts and programs
• Hands‑on experience with pharmacophores
• Proven expertise in applying molecular modeling methods to structure-based and/or ligand-based drug discovery
• Thorough understanding of molecular recognition principles
• Thorough understanding of the drug design literature
• Hands‑on experience with a broad range of computational methods, including virtual screening, programming, statistical analysis, data analysis, molecular docking, molecular dynamics, and ADME modeling
• Deep knowledge of advanced computational chemistry techniques, including FEP, ML, and QSAR

The base pay range for this position at commencement of employment is expected to be between $180K and $220K a year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.