Flagship Pioneering

Senior Scientist, Small Molecule Screening

Flagship Pioneering • $126K — $181K *
Pharmaceuticals & Biotech
5 - 7 years of experience
Job Overview by Ladders

Qualifications

  • Ph.D. in organic chemistry, medicinal chemistry, or chemical biology with 5+ years of relevant experience.
  • End-to-end expertise in DNA-encoded library (DEL) processes, from design to hit validation.
  • Hands-on experience with DNA-compatible chemistry, including split-and-pool synthesis.
  • Familiarity with encoding strategies, analytical quality control, and LC-MS.
  • Experience with various affinity selection formats and controls.
  • Capable of managing contract research organizations (CROs).
  • Preferred: cheminformatic skills, laboratory automation, and microfluidics.

Responsibilities

  • Develop technology aligned with strategic company goals, influencing scientific direction.
  • Design and construct DNA-encoded small molecule libraries with quality control.
  • Execute affinity-based selections against protein targets, ensuring analysis of control selections.
  • Deconvolute and validate screening hits, confirming activity through off-DNA resynthesis.
  • Optimize workflows and document best practices for platform excellence.
  • Ensure timely and accurate data turnaround to meet project objectives.
  • Translate experimental results into insights and present findings in team settings.

Benefits

  • Early employee opportunity to establish a transformative scientific platform.
  • Custom-tailored role for impactful contributions and professional growth.
  • Weekly lunches, monthly social events, and community lunchroom with free snacks and coffee.
Full Job Description
Position Summary:

We are seeking a motivated and highly collaborative Senior Scientist to join FL129's growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have a strong track record of scientific and technical innovation in DNA-encoded library (DEL) design, synthesis, and affinity-based selection. Deep experience with DNA-compatible chemistry and with hit deconvolution and validation is essential, and additional experience with cheminformatic analysis of chemical space and library diversity is strongly desired. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment.

Key Responsibilities:
  • Technology development, aligned with FL129's core strategic goals. This role is among the first hires, and we're looking for someone who thinks critically and will influence the company's scientific direction.
  • Design, construction, and quality control of DNA-encoded small molecule libraries, including building-block selection and validation
  • Execute and optimize affinity-based selections against protein targets, including appropriate control selections and enrichment analysis
  • Deconvolute and validate screening hits, including off-DNA resynthesis and confirmation of activity
  • Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
  • Ensuring rapid and accurate turnaround of data to drive achievement of key project goals.
  • Translate experimental data into meaningful insights and present results at team meetings.

Preferred Qualifications:
  • Ph.D. in organic chemistry, medicinal chemistry, chemical biology, or a similar field with 5+ years of industry or postdoctoral experience.
  • End-to-end experience with DNA-encoded library (DEL) screening, from library design and synthesis through affinity selection, next-generation sequencing, and hit deconvolution.
  • Hands-on expertise in DNA-compatible chemistry, including split-and-pool combinatorial synthesis, building-block validation, and development or adaptation of reactions to on-DNA conditions.
  • Experience with encoding and tagging strategies, including barcode design and enzymatic ligation, and with analytical quality control of library synthesis (e.g., LC-MS).
  • Experience with affinity selection formats and their controls, including immobilized and solution-phase targets, matrix and negative selections, and DNA-encoded positive controls.
  • Experience with on-DNA and off-DNA hit validation, including resynthesis and biochemical/biophysical assays to confirm and quantitate the bioactivity of screening hits.
  • Experience managing contract research organizations (CROs).
  • Nice to have: cheminformatics experience, including library enumeration and chemical space or diversity analysis; droplet-based screening and/or microfluidics; and laboratory automation and liquid handling.
  • Motivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills.

What we can offer you:
  • Opportunity to lay the scientific foundation of a transformative platform company as an early employee.
  • Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
  • Weekly lunches, monthly social events, and community lunchroom with free snacks, coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. FL129 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL129's good faith estimate as of the date of publication and may be modified in the future.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

Similar Jobs

More Jobs at Flagship Pioneering

More Pharmaceuticals & Biotech Jobs

Find similar Senior Scientist, Small Molecule Screening jobs: