Job Title: Principal Scientist, Computational Chemistry

Job Number: 24210

Location: Cambridge, MA

Job Description

We are looking for an experienced Computational Chemist to help transform initial hits from our De Novo Discovery platform into lead compounds with appropriate drug-like properties.  With the support of top-tier peptide chemists, medicinal chemists and informatics scientists, the incumbent would be responsible for setting the standard for how FogPharma leverages innovative computational approaches to develop a lead compound.  The quick design-synthesize-test cycle enabled by our Helicons means that new approaches can be tested and improved rapidly.  This is an exciting opportunity to develop and implement a computational chemistry strategy at a growing company using a novel technology platform to make a substantial impact for patients with intractable diseases.


  • Help develop the company’s computational chemistry strategy to accelerate hit-to-lead progression.
  • Perform analyses linking sequence and chemical structure of macrocyclic peptides with measured properties to enable design of peptides with desired properties and activities.
  • Devise and implement machine learning approaches to accelerate understanding and design of macrocyclic peptides.
  • Identify chemoinformatic tools to enable peptide library design for maximal diversity of chemical space with regards to multiple chemical properties relevant to macrocyclic peptides.
  • Advise data management engineers on requirements for data storage and access to enable analysis and reporting of structure-activity and structure-property relationships.
  • Provide optimal visualization of large datasets to facilitate quick decision-making and fast cycle-time.
  • Identify/apply predictive tools for metabolic liabilities of macrocyclic peptides.
  • Explore correlation between in silico and measured physicochemical properties
  • Perform in silico conformational analysis and structure-based drug design and modeling of alpha-helical macrocyclic peptides.

Required Skills

  • PhD. in Chemoinformatics, Computational Chemistry, Biophysics, or related field with 7+ years of industry experience in pharmaceutical/biotech setting required.
  • Demonstrated track record of success developing and using computational tools to advance discovery programs from target validation through lead optimization.
  • Expert knowledge of modern methods of peptide and medicinal chemistry with ability to successfully and simultaneously conduct medicinal chemistry on multiple projects.
  • Experience with peptide drug development and structure-based drug design (SBDD) are a plus.
  • Ability to independently solve problems as part of a fast-paced team.
  • Capacity to execute tasks independently to achieve company goals on an established timeline.
  • Excellent communication, organization, multi-tasking, flexibility and team skills.
  • Enthusiasm to work in a dynamic research environment.


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