Cheminformatics Jobs in Boston, MA (NOW HIRING)

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!

FL111 is seeking a Director/Senior Director, Computational Chemistry to spearhead the design and optimization of heterobifunctional small molecules. This leader will work closely with medicinal chemists, structural biologists, and project teams to develop and apply computational tools to guide molecular design decisions across the design–build–test–learn cycle. The successful candidate will drive molecular ideation, property optimization, and compound prioritization across the portfolio. This is a strategic, high-impact leadership role where the Director/Senior Director will shape computational strategy, drive scientific excellence, and help build and mentor a world‑class computational chemistry function.

• Molecular Design & Optimization: Define the strategic vision for and drive the design of heterobifunctional small molecules, including ligand selection, attachment vectors, and linker architectures, integrating cross-functional input to balance target engagement, molecular properties, and synthetic efficiency across programs.
• Cheminformatics & Library Exploration: Lead and direct cheminformatics strategy to identify and prioritize chemical series; oversee development of internal computational workflows and data infrastructure to support program needs
• ADME & Developability Assessment: Direct evaluation of key molecular properties (e.g., solubility, permeability, lipophilicity, clearance risk) and lead compound prioritization frameworks that systematically integrate developability considerations across the portfolio.
• Structure-Based & Computational Modeling: Champion and advance structure‑based and AI/ML‑assisted modeling capabilities (e.g., docking, conformational analysis, FEP) to inform ligand selection, attachment strategy, and linker design; drive adoption of emerging computational methods across the organization.
• Cross‑Functional Collaboration: Serve as a strategic scientific partner and computational chemistry leader across chemistry, biology, and in vivo pharmacology teams within the company; align on portfolio priorities, and represent the computational chemistry function in leadership discussions and external scientific forums.

• PhD in Chemistry, Medicinal Chemistry, Computational Chemistry, or a related discipline, with 10+ years of relevant industry experience, including demonstrated scientific leadership and people management experience.
• Deep expertise in computational medicinal chemistry and structure‑based drug design in the binary and ternary settings, with a track record of driving impactful decisions across multiple drug discovery programs.
• Demonstrated ability to drive and evaluate real, synthetically actionable molecular designs and to mentor and develop scientists to do the same.
• Experience using cheminformatics tools for compound design, analysis and prioritization.
• Proven scientific leadership and communication skills: demonstrated ability to build, lead, and inspire interdisciplinary teams and influence senior stakeholders.
• 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.

Location: Cambridge, MA

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.

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 - $294,300. 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.

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 your 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 privacy@flagshippioneering.com.