Computational Chemist

Location: Cambridge MA

Cambridge, MA-based H3 Biomedicine (H3B) is a leading company in cancer genomics driven drug discovery, delivering on the promise of precision medicine. The company was launched in 2011 with an unprecedented $200 million in initial funding from Eisai, plus a continued ongoing commitment to fund H3B’s robust discovery pipeline and clinical programs. Now with four clinical stage anti-cancer molecules in active development, H3B is able to uniquely leverage distinct insights from cancer genomics and real-life patient data to advance its projects to clinical proof of concept and beyond. H3B embraces a novel business model in which it collaborates with Eisai, a leading global pharmaceutical company, to create a prolific drug discovery engine and partnership platform.

We are looking for a computational chemist with robust knowledge and proven skill sets of molecular modeling underpinned by significant experience and passion in working with colleagues toward H3 Biomedicine’s vision.  A key element of her/him is a strong interest in data- and hypothesis- driven drug discovery by applying state-of-the-art computational chemistry methods, including structure- and ligand-based design, virtual screening, free energy simulation, and molecular dynamics.  As a key member of a project, she/he is expected to work independently and demonstrate scientific leadership and creativity within a multi-disciplinary environment.

Principal Duties and Responsibilities
  • Work with a high degree of independence to carry out structure and ligand-based design and data analysis
  • Support all aspects of the company’s computational chemistry efforts across, targeting multiple cellular pathways/mechanism and indications
  • Implementation of computational chemistry toolkits (e.g. MOE, MolSoft, OpenEye, Schrodinger)
  • Develop and implement computational chemistry approaches to design and triage compound ideas
  • Closely collaborate and communicate with medicinal chemists to understand current issues and provide most effective solutions
  • Proactively propose strategies for effective use of computational chemistry to accelerate hit-to-lead and lead optimization toward clinical candidates
  • Develop and introduce structure-based methods that potentially enhance H3’s design capability of new modality targets, including allosteric modulators, PROTACs, and glues of protein-protein interactions.
  • Create strategies of machine learning/AI through communication with global colleagues and exploit the methodologies to implement a more effective design environment in H3
  • Stay up to date with cutting-edge computational chemistry, in particular structure-based drug design and machine learning/AI through continuous exposure to the latest information available from related journals and symposiums
  • Participate in interdisciplinary teams and external collaborations
  • Identify and solve significant problems related to projects/discipline
  • Effectively communicate and present research results across multiple disciplines
  • Coordinate with collaborators, consultants, and contract services to improve research projects in a transparent, timely, and consistent manner
  • Work in a fast-paced/small-team environment that is growing and evolving and which requires regular reprioritization of projects while adhering to timelines and achievement of deliverables
  • Show initiative to expand scope and depth of technical competence
  • Good interpersonal skills, flexibility, and work well within a team environment
  • The position requires a Ph.D. in computational chemistry or related discipline with 10+ years in the biotech/pharmaceutical industry. Advanced knowledge of medicinal and computational chemistry principles and knowledge of how to apply these techniques to drug discovery projects
  • Practical experience in structure-based drug design, including docking, homology modeling, molecular dynamics simulation, and free energy calculation; ligand-based drug design, including pharmacophore modeling, QSAR, 3D-QSAR, pharmacophore- or shape-based database searching, combinatorial library design, and target focused library construction
  • Proven track record in making visible and significant impact on drug discovery projects through collaboration with chemistry and biology colleagues
  • Experience in application of molecular dynamics for novel modality targets, including allosteric modulators, PROTACs, and glues of protein-protein interactions will be highly desirable.
  • Ability to multitask and support multiple projects simultaneously
  • Willingness to proactively suggest most suitable computational chemistry solutions for project issues
  • Proven competency in one or more molecular modeling suites (Schrodinger, Openeye, and MOE) is essential
  • Robust understanding of Linux command line is required
  • Strong programming/scripting capabilities (Schrodinger/OEChem python and machine learning API, including Scikit-learn and Tensorflow) will be desirable
  • Experience with effective leadership of functional and/or project teams and strategic planning in a small to large biotechnology company
  • A proven record of scientific leadership and innovation as demonstrated by publications, presentations, and / or patents
  • Excellent communication and organizational skills are required
  • Experience managing external collaborations, including CRO’s
About H3 Biomedicine Inc.

H3 Biomedicine Inc. is a privately-held, uniquely-structured oncology discovery enterprise whose sole mission is to become a prolific source of new drugs that treat more human cancers with greater success. H3 Biomedicine is applying the expertise of leading scientists to the integration of insights from cancer genomics with innovative capabilities in synthetic chemistry and tumor biology to pursue the most promising current opportunity in cancer therapeutics: patient-based, genomics-driven, small molecule drugs.

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