Job Description

Job Description

Job Description

Arrowhead Pharmaceuticals, Inc. (Nasdaq: ARWR) is a clinical stage biopharmaceutical company that develops medicines that treat intractable diseases by silencing the genes that cause them. Using a broad portfolio of RNA chemistries and efficient modes of delivery, Arrowhead therapies trigger the RNA interference mechanism to induce rapid, deep, and durable knockdown of target genes. RNA interference, or RNAi, is a mechanism present in living cells that inhibits the expression of a specific gene, thereby affecting the production of a specific protein. Arrowhead's RNAi-based therapeutics leverage this natural pathway of gene silencing.

Arrowhead is focused on developing innovative drugs for diseases with a genetic basis, typically characterized by the overproduction of one or more proteins that are involved with disease. The depth and versatility of our RNAi technologies enables us to potentially address conditions in virtually any therapeutic area and pursue disease targets that are not otherwise addressable by small molecules and biologics. Arrowhead is leading the field in bringing the promise of RNAi to address diseases outside of the liver, and our clinical pipeline includes disease targets in the liver and lung with a promising pipeline of preclinical candidates.

Arrowhead's corporate headquarters is in Pasadena, CA with research and development teams in Madison, WI & San Diego, CA, and a state of the art manufacturing facility in Verona, WI. Our employees are nimble, science-driven innovators who are collaborating to bring new therapies to patients in need.

The Position

We are seeking a highly skilled Computational Chemist with strong molecular dynamics expertise to join our dynamic team in Madison, Wisconsin. In this on-site role, you will apply MD simulations to accelerate oligonucleotide drug development, advance predictive power of AI/ML models and explore novel spaces in oligonucleotide drug design. You will work closely with a cross-functional R&D team at the cutting edge of RNA interference (RNAi), where your computational insights will directly impact the development of life-changing therapies.

Responsibilities

• Molecular Dynamics Simulation of RNA protein interactions: Analyze large biological datasets (sequences, structures, activity data) to uncover patterns and insights that inform lead discovery. Apply state-of-the-art methods to elucidate mechanisms of RNA protein interaction that underpin empirical understanding of gene silencing.
• Machine Learning R&D: Apply learnings to aid in creating AI/ML frameworks and explore novel chemical space in oligonucleotide drug design. Cross-Functional
• Collaboration: Work closely with chemists, biologists, and other scientists to integrate computational designs with experimental validation. Propose candidates and provide in-silico rationale for compounds to be synthesized or biologically tested, and iteratively improve designs based on lab results.
• Innovation & Continuous Learning: Stay up-to-date with the latest research and advancements in AI/ML for drug discovery (e.g. new algorithms, frameworks, and scientific publications). Evaluate and integrate new tools or methodologies (for example, improved protein structure prediction algorithms or generative models) to continually enhance the team's capabilities.

Requirements

• Ph.D. in a relevant field (Computational Chemistry, Physics, Biochemistry, Bioinformatics, Computer Science, or related discipline) with a focus on computational approaches in chemistry or biology. Research focus in molecular dynamics is preferred . Candidates with 0–10 years of postdoctoral or industry experience (including recent PhD graduates) are encouraged to apply.
• Molecular Dynamics Expertise: Demonstrated experience in physical modeling and molecular dynamics (MD) simulations using GROMACS, AMBER, OpenMM, or similar tools. Solid understanding of algorithms for modeling molecular structures or properties, and familiarity with statistical modeling and data science in a scientific context.
• Programming Skills: Proficiency in Python programming and common scientific computing libraries. Ability to develop and debug code for dynamic workflows; experience with version control (Git) and reproducible research practices. Experience in scripting and workflow automation for simulation setup, monitoring, and analysis.
• Collaborative Skills: Excellent problem-solving abilities and communication skills. Proven ability to work both independently and as part of an interdisciplinary team, effectively communicating computational findings to collaborators from chemistry and biology backgrounds.

Preferred

• Experience in combining physics-based modeling approaches with machine learning or AI is a strong plus.
• Demonstrated expertise in applying free energy calculation methods—such as FEP, TI, MM/PBSA, or MM/GBSA—to biologically and pharmaceutically relevant targets, with an emphasis on quantitative binding affinity prediction or selectivity profiling.
• Proven experience leveraging molecular dynamics simulations to support drug discovery efforts in an industry setting, including applications in lead optimization, target validation, and mechanistic hypothesis testing.

Wisconsin pay range

$105,000—$120,000 USD

Arrowhead provides competitive salaries and an excellent benefit package.

All applicants must have authorization to work in the US for a company.

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