Associate Director, Computational Chemistry

Associate Director, Computational Chemistry Protagonist Therapeutics - 4.0 Newark, CA Job Details $180,000 - $220,000 a year 1 day ago Qualifications Databases Drug discovery

Doctor of Philosophy Scripting Full Job Description Associate Director, Computational Chemistry Job Description:

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.

Duties and Responsibilities include:

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

Requirements:

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. Protagonist Therapeutics is a discovery through late-stage development biopharmaceutical company. The Company's proprietary peptide technology platform enables de novo discovery of peptide therapeutics. Two novel peptides derived from Protagonist's proprietary discovery platform are at or near commercialization. ICOTYDE™ (icotrokinra) is approved in the U.S. for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age and older who weigh at least 40 kg who are candidates for systemic therapy or phototherapy. ICOTYDE is the first and only targeted oral peptide that precisely blocks the Interleukin-23 receptor (IL-23R) licensed to Janssen Biotech, Inc.,a Johnson & Johnson company. ICOTYDE was jointly discovered by Protagonist and Johnson & Johnson scientists, with Protagonist having primary responsibility for the development of ICOTYDE through Phase 1, and Johnson & Johnson assuming responsibility for further development and commercialization. An NDA for rusfertide, a first-in-class hepcidin mimetic peptide that is being co-developed with Takeda Pharmaceuticals pursuant to a worldwide license and collaboration agreement entered in 2024, is under priority review with the FDA. Protagonist holds an option to co-commercialize rusfertide in the U.S. through a 50/50 profit and loss share structure or can opt-out of this structure. The Company also has a number of preclinical stage drug discovery programs addressing clinically and commercially validated targets including an oral IL-17 peptide antagonist, obesity dual and triple agonists, an oral hepcidin functional mimetic, and the recently announced IL-4 and amylin programs. More information on Protagonist, its pipeline drug candidates, and clinical studies can be found on the Company's website at https://www.protagonist-inc.com.