Associate Director/Director, Computational Chemistry

COMPANY DESCRIPTION
 
Flagship Labs 111 Inc. (FL111) is a privately held, early-stage biotechnology company pioneering a novel platform harnessing innovations in chemistry, computation, and data science to create new therapeutic modalities beyond traditional small molecules. FL111 is backed by Flagship Pioneering, bringing the courage, vision, and resources to guide FL111 from platform validation to patient impact. We are seeking collaborative, creative and relentless problem solvers that share our passion for impact to join us! 

THE ROLE

FL111 is seeking an AD/D, Computational Chemistry to play a central role in the design and optimization of heterobifunctional small molecules. This individual will work closely with medicinal chemists, biologists, and in vivo pharmacologists to develop and apply computational tools to guide molecular design decisions across the design–build–test–learn cycle. The successful candidate will contribute directly to molecular ideation, property optimization, and compound prioritization, with a particular focus on the unique challenges of heterobifunctional molecules. This is a hands-on, high-impact role in a fast-paced startup environment where computational insights directly shape experimental strategy.

KEY RESPONSIBILITIES

• Molecular Design & Optimization: Propose & evaluate heterobifunctional small molecule designs, including ligand selection, attachment vectors, and linker architectures, with a strong focus on balancing target engagement, molecular properties, and synthetic efficiency.
• Cheminformatics & Library Exploration: Perform cheminformatics analyses to identify chemical series that enable improved property profiles and simplified syntheses
• ADME & Developability Assessment: Evaluate and predict key molecular properties (e.g., solubility, permeability, lipophilicity, clearance risk) and help prioritize compounds by integrating developability considerations.
• Structure-Based & Computational Modeling: Apply structure-based modeling tools (e.g., docking, conformational analysis) to inform ligand selection, attachment strategy, and linker design, translating computational insights into clear, actionable design recommendations.
• Cross-Functional Collaboration: Work closely with chemistry, biology, and in vivo pharmacology teams to guide experimental planning, inform design–make–test cycles, and communicate computational insights clearly in project discussions and presentations.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline, with 5+ years of relevant industry experience (or equivalent experience).
• Hands-on experience in computational medicinal chemistry or structure-based drug design.
• Demonstrated ability to propose and evaluate real, synthetically actionable molecular designs.
• Experience using cheminformatics tools for compound design, analysis and prioritization.
• Strong collaboration and communication skills: ability to work effectively in interdisciplinary teams.
• Prior experience working on heterobifunctional small molecules (e.g., PROTACs) is preferred
• Familiarity with ADME optimization challenges for large, flexible molecules is strongly preferred.
• Prior experience in an early-stage or startup biotech environment is preferred.

About Flagship Pioneering

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering is 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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.

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The salary range for this role is $176,000 - $253,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL111 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL111's good faith estimate as of the date of publication and may be modified in the future.