Lead Computational Chemist - Molecular Design & ML

Antares Therapeutics; Boston; On-site; PHP 11,412,707 - 14,805,674; Full time

Job summary

Antares Therapeutics in Boston, MA is seeking a highly experienced computational chemist to lead solution-driven design across discovery programs. You will apply structure- and ligand-based design, MD, and FEP to advance small‑molecule leads while shaping the computational platform and collaborating with multidisciplinary teams.

The role, offered at Principal/Senior Principal Scientist level, requires deep domain expertise, leadership, and a track record of influencing programs and external

Qualifications

• PhD in computational chemistry, biophysics, theoretical chemistry, pharmaceutical sciences, cheminformatics, or a related quantitative field (or equivalent experience).
• Principal Scientist: PhD with 10+ years (or bachelor's with 16+ years) of computational chemistry experience in a pharmaceutical and/or biotechnology setting. Senior Principal Scientist: PhD with 12+ years (or bachelor's with 18+ years), with a demonstrated track record of independent scientific leadership, cross-functional influence, and organizational impact.
• Demonstrated, direct contributions to drug discovery programs through the application of computational chemistry — ideally including progression of compounds into or toward the clinic.
• Deep, hands‑on expertise across modern computational methods: structure- and ligand-based design, molecular dynamics, and free energy methods (e.g., FEP).
• Experience applying machine‑learning and/or generative molecular design methods in a discovery setting is strongly preferred.
• Experience in covalent drug discovery — including covalent docking, warhead selection and reactivity/selectivity assessment, and modeling of covalent kinetics (e.g., kinact/Ki) — is strongly preferred and is central to Antares' programs.
• Proficiency with the Schrödinger suite and/or comparable platforms (e.g., MOE, OpenEye), and programming/scripting in Python and with coding assistants like Claude Code/Codex for cheminformatics and data analysis.
• Strong understanding of medicinal chemistry, structural biology, and DMPK principles, and a proven ability to collaborate effectively in a fast‑paced, matrixed, team‑based environment.
• Excellent written and verbal communication skills, with the ability to convey complex computational concepts to multidisciplinary audiences.
• A passionate, results‑oriented drug hunter who thrives in a collaborative, data‑driven, and scientifically ambitious culture.

Responsibilities

• Serve as the computational chemistry function lead on programs, providing integrated leadership across target validation, hit identification, hit-to-lead, and lead optimization for multiple small-molecule programs.
• Apply structure-based and ligand-based design, molecular dynamics, and free energy perturbation (FEP) to prioritize compounds, evaluate druggability, and identify and exploit cryptic or novel binding pockets on challenging targets.
• Integrate machine-learning, generative, and active-learning approaches into design-make-test-analyze cycles, and multiparameter optimization of potency, selectivity, and ADMET/physicochemical properties.
• Partner closely with medicinal chemistry to translate computational hypotheses into synthesized, tested molecules, and to drive sound decision-making and smart risk-taking.
• Lead computational infrastructure and platform development — identifying, evaluating, and deploying best-in-class tools, methods, and workflows — and contribute to major collaborations with external partners, in coordination with the Discovery Predictive Sciences team.
• Analyze and integrate data across functions to independently identify, define, and address critical scientific issues and key scientific questions.
• Communicate analyses, models, and recommendations clearly to project teams and leadership, influencing program strategy and portfolio decisions.
• Represent computational chemistry in cross-functional program teams; help set design strategy and define the questions that computation should answer at each stage.
• Mentor junior scientists and, at the Senior Principal level, provide broad scientific direction, establish best practices, and act as a recognized technical authority internally and in the external scientific community.

Job description

Antares Therapeutics in Boston, MA is seeking a highly experienced computational chemist to lead solution-driven design across discovery programs. You will apply structure- and ligand-based design, MD, and FEP to advance small‑molecule leads while shaping the computational platform and collaborating with multidisciplinary teams.

The role, offered at Principal/Senior Principal Scientist level, requires deep domain expertise, leadership, and a track record of influencing programs and external