Scientist, Computational Chemistry (CompSci0003)

South San Francisco, California
Commensurate with qualifications and experience
Aug 03, 2018
Required Education
Position Type
Full time

Circle Pharma is an emerging biotech company discovering and developing macrocycle therapeutics targeting important intracellular protein-protein interactions. Our novel, intrinsically cell-permeable macrocycles provide a unique opportunity to address these “undruggable” targets.  Our first targets are in molecularly defined cancers, with future expansion to other therapeutic areas. 

We are a tightly integrated team of synthetic and computational medicinal chemists and pre-clinical biologists. Our discovery platform includes structure based design, integrating target affinity, cell permeability and medicinal chemistry, and automated macrocycle synthesis. We have open positions for candidates who want to make key contributions to a small, exciting startup company and help drive its growth.  For more information about Circle Pharma, see our website at

Job Description

We are seeking a highly skilled and motivated Computational Chemistry Scientist with a strong background in computational drug discovery and informatics. This individual will engage in drug discovery enabled by our computational/medicinal chemistry and biology group; will use and expand both internally developed and commercial tools to perform computer-aided design of cell permeable macrocycles; and have a strong desire to learn new techniques and incorporate new methodologies into their work.  The ideal applicant will have demonstrated expertise in current computational drug design and chemical information workflows, along with possessing a high level of creativity, knowledge of reaction mechanisms, and strong problem-solving skills

Key Responsibilities

  • Manage and analyze chemical information workflows
  • Collaboratively design, construct and evaluate targeted and general macrocycle virtual libraries for target engagement and cell permeability
  • Undertake macrocycle identification and optimization efforts, including structure-based design, QSAR, and target-based selection of building blocks that meet specific physico-chemical and biological activity criteria
  • Assist with development of customized computational algorithms
  • Maintain currency with literature in computational medicinal chemistry

Minimum Requirements

  • Ph.D. in Computational Chemistry, Computational Biology, Biophysics or related field with at least 3 years of experience in small molecule discovery and development in the biotech/pharmaceutical industry
  • Unix/Linux and scripting experience (Perl and Python)
  • Trained in computational approaches to drug design, lead optimization, protein engineering or protein structure prediction
  • Experience with conformational analysis of macrocycles
  • Experience with chemical informatics software tools
  • Experience modeling protein-ligand binding interactions using structure-based and ligand-based methods
  • Excellent written and verbal communication skills
  • Comfortable with independent problem solving in a collaborative environment
  • Proficient in the use of Microsoft Office and ChemDraw
  • Strong organizational, communication, and interpersonal skills 
  • Team-oriented and works well in collaborative environments 
  • Excel at maintaining laboratory record of scientific findings
  • Self-motivated, independent, and have the ability to work with minimal supervision
  • Enjoy operating in an exceptionally dynamic, high-achieving and cooperative environment where every voice matters
  • Be able to lift 20 pounds comfortably

Preferred Qualifications

  • Experience with Schrodinger software (Prime, Glide, Phase)
  • Experience with pipelining tools such as Knime
  • Experience with data and statistical analysis software

Circle Pharma is a dynamic start-up company, and the successful candidate must have the ability and desire to work in a fast-paced environment. Circle offers a comprehensive compensation package, as well as generous paid time off in addition to Company observed holidays.  The Company provides Medical, Dental and Vision Insurance, along with a retirement savings plan which includes employer contributions.  We promote a culture in which employees are respected and rewarded for hard work, innovation, personal initiative, and teamwork. 

Circle Pharma is an equal opportunity employer and committed to a diverse workplace. All applicants will be considered equally without regard to race, color, ethnicity, veteran status, religion, national origin, marital status, political affiliation, age, sex, sexual orientation, handicapping condition, membership in an organization or any other non-merit factors.

Qualified candidates are encouraged to submit a Resume/CV and cover letter to Cayla McEwen via email at info@circlepharma.comand please refer to job code CompSci0003 in the subject line. No phone calls please. Direct applicants only.