Senior Scientist, Small Molecule Screening

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 126,000 - 182,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Labs FL129, a Flagship Pioneering venture, seeks a Senior Scientist to build a novel DEL platform. You will lead experimental and computational efforts, shaping the platform’s direction and contributing from day one in a highly collaborative setting.

The role demands strong experience in DEL design, synthesis, hit validation, and chemoinformatic analysis, with the ability to communicate results across multidisciplinary teams and to drive platform excellence.

Qualifications

• Ph.D. in organic chemistry with 5+ years of industry or postdoctoral experience.
• End-to-end experience with DNA-encoded library (DEL) screening, including design, synthesis, affinity selection, and hit deconvolution.
• Hands-on DNA-compatible chemistry, including split-and-pool synthesis and on-DNA reactions.
• Experience with encoding and tagging strategies, barcode design, and enzymatic ligation.
• Experience with affinity selection formats, controls, and DNA-encoded positive controls.
• Experience with on-DNA and off-DNA hit validation, including resynthesis and biochemical/biophysical assays.
• Experience managing contract research organizations (CROs).
• Nice to have: cheminformatics, library enumeration, diversity analysis; droplet-based screening; laboratory automation; and liquid handling.
• Motivated team-player with strong organizational and written/verbal communication skills.

Responsibilities

• Technology development aligned with FL129’s strategic goals and influence on scientific direction.
• Design, construction, and quality control of DNA-encoded small molecule libraries, including building-block validation.
• Execute and optimize affinity-based selections against protein targets with appropriate controls.
• Deconvolute and validate screening hits, including off-DNA resynthesis and activity confirmation.
• Optimize workflows and establish documentation practices to enable platform excellence.
• Ensure rapid turnaround of data to drive achievement of key project goals.
• Translate experimental data into insights and present results at team meetings.

Skills

DEL design

DEL synthesis

Affinity-based selection

Hit deconvolution

DNA-compatible chemistry

Barcode design

Enzymatic ligation

Cheminformatics

Team collaboration

Scientific communication

Education

Ph.D. in Organic Chemistry

Tools

LC-MS

Next-Generation Sequencing

Job description

What if…you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering. This is a hands‑on role with substantial ownership for a scientist who is excited to set technical direction from day one and, over time, help build the team.

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.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

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.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].