Associate Director, Computational Chemistry/Cheminformatics

Computational Drug Discovery · Waltham, Massachusetts
Department Computational Drug Discovery
Employment Type Full-Time
Minimum Experience Senior Manager/Supervisor

Do you have the passion to join a group whose mission is to pioneer the discovery of a new class of medicines to treat diseases unaddressed by today’s therapies? Does it excite you to be a part of a company with a focus on cancer and genetically validated targets in other disease areas with unmet medical need? If yes, you may be a great fit to join Arrakis on our path to bring powerful new therapies to millions of patients. 

Your Impact at Arrakis

The mission of Arrakis Therapeutics is to extend small molecule drug discovery into new realms of biology by discovering and developing compounds that selectively target RNA. By targeting specific RNA structure/function relationships, Arrakis will generate drug candidates with novel mechanisms of action for high-value molecular targets that are challenging to address via more traditional protein-centric approaches. Our efforts span a wide range of disease areas including oncology, neuroscience and rare disease, with a focus on indications with high unmet medical need.


Arrakis is seeking a computational chemist to join our rapidly growing company in pursuit of targeting RNA with small molecules.  The successful candidate will support all aspects of medicinal chemistry programs from hit to lead and beyond, participate in computational informatics strategies, interface with consultants and collaborate across disciplines within Arrakis. The ideal candidate will enjoy working in a collaborative, fast-paced start-up environment, leveraging a high degree of integrity, intelligence and innovation to make a large impact on our mission.


Job Responsibilities:


  • Lead and mentor direct reports to produce high-quality results while fostering a positive work environment
  • Contribute to company strategies including, but not limited to, portfolio management and state-of-the-art modeling and informatics for molecular design hypotheses
  • Provide computational medicinal chemistry support towards, but not limited to, hit-to-lead progression, initiating new projects, and new drug-target assessments


  • PhD in Chemistry, Computational Chemistry, Biophysics or related scientific field with 8+ years of experience within pharmaceutical or biotechnology field
  • Demonstrated mastery of modern computational chemistry including, but not limited to, structure-based design (receptor and ligand-based), scaffold hopping, docking and conformational analysis
  • Cheminformatics expertise, such as modern AI and machine learning, chemical reaction/library enumeration, 2D/3D similarity, clustering, dimensionality reduction techniques that are related to data mining and data visualizations
  • Experience with enterprise informatics systems such as Knime, SQL databases and data warehouses
  • Expertise with macro biomolecular modeling that may be transferable to RNA structure by incorporating constraints from NMR, CryoEM or other structural, biochemical data (RNA modeling experience a plus)
  • Strong scientific programming skills (Python preferred) and pipelining tools, (e.g. Knime) in a Linux environment.
  • Familiarity with cloud computing environments (Google, AWS)
  • An understanding of modern drug discovery including medicinal chemistry and DMPK principles, basic tox and multi-parametric optimization, molecular recognition principles, and the ability to adapt and translate these principles to RNA 


Interested in learning more about Arrakis?  Click on the links below!



Arrakis is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive equal consideration for employment without regard to race, color, religion, national origin or ancestry, sex, pregnancy, sexual orientation, gender identity, age, disability, military service, veteran status, genetic information, or any other characteristic protected by law.

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  • Location
    Waltham, Massachusetts
  • Department
    Computational Drug Discovery
  • Employment Type
  • Minimum Experience
    Senior Manager/Supervisor