Target Gallery

Beryllium announces the signing of a structural biology collaboration with Deciphera Pharmaceuticals.  Under the terms of the agreement, Beryllium will provide gene-to-structure research information on multiple kinase targets and deliver high-resolution crystal structures to support Deciphera’s kinase inhibitor discovery activities.

“Deciphera’s collaboration with Beryllium exemplifies our commitment to advancing improved treatment options for patients with cancer,” said Daniel Flynn, Ph.D., Chief Scientific Officer at Deciphera Pharmaceuticals.  “Beryllium’s expertise in structure-directed drug discovery coupled with Deciphera’s proprietary switch control kinase inhibitor platform offers the potential to accelerate the delivery of tumor-targeted therapies and immuno-targeted therapies to improve human health.”

“At Beryllium we are very excited to partner with Deciphera, an industry leading oncology therapeutics company,” said Johan Pontin, Chief Executive Officer at Beryllium Discovery.  “Deciphera’s cutting edge research in kinase inhibitors dovetails with Beryllium’s gene to structure expertise and together we will unlock the therapeutic potential of new oncology targets.”


About Beryllium


Using a biology-first, target-centric approach and established platforms, Beryllium provides research services and engages in collaborations with commercial and academic partners.  Beryllium’s teams of experienced scientists work closely with drug discovery clients to help manage and advance their goals by complementing their capabilities and resources.


Media Contact: Mark Schmeizl, Beryllium Discovery,

Our Bedford, MA facility has an opening for a Research Scientist in our Protein Expression Core.  The successful candidate will perform advanced laboratory activities primarily using mammalian expression systems.  The successful candidate will possess fermentation and cell culture expertise (small and large scale) and excel in a fast-paced environment.



  • All methods and techniques required for protein expression and optimization experiments in mammalian, insect and bacterial expression systems from small scale to production scale with strong aseptic techniques
  • Develop methods for high yield expression of novel target proteins
  • Perform multiple experiments with multiple targets in parallel under aggressive timelines
  • Provide support to the Group Leader regarding production planning
  • Follow, develop and implement Site Work Procedures
  • Lead and mentor junior scientists
  • Collaborate with other Core lab functions
  • Analyze and present data in meetings and to external audience as needed


Education and Experience:

  • A life science degree with at least 6 years’ experience in recombinant protein expression
  • Impeccable communication skills
  • Advanced lab skills in recombinant protein expression for a variety of proteins, cell types and expression systems
  • Solid experience with mammalian cultures
  • Understanding of protein expression/purification workflows along with production experience
  • Assay experience is a plus

Our Bedford, MA facility has an opening for a Group Leader to lead our Protein Expression Core.  The successful candidate will be a proven leader and an individual who can develop and manage the Protein Expression team on projects involving fermentation/bacterial, baculoviral/insect cell and mammalian protein expression systems in support of early discovery to early development/structural studies. Candidates must have strong protein expression and protein engineering skills using different expression systems coupled with an understanding of cell engineering, cell biology and molecular biology. This position will have the opportunity to make a significant scientific contribution to drug discovery projects. Communication will be key within the Core and across multiple disciplines.




  • Work collaboratively with other disciplines to meet aggressive project deliverables and timelines and ensure projects are completed with a high degree of accuracy and production does not falter; determine courses of action and troubleshoot when there are issues with experiments;
  • Manage, mentor and support career development of Protein Expression staff to maximize individual and team performance. Engage in laboratory work when appropriate and set the scientific standards within the Core. Assist with transition to a 24/7 operational schedule.
  • Identify, evaluate, develop and integrate new protein expression-related technologies; challenge and mentor team members to perform more advanced experiments, analysis, troubleshooting.
  • Review documents including technical reports, SOPs, SWPs, and method validation and transfer protocols and reports. Update and author documents as necessary.
  • Identify process deviations, prepare technical reports and propose comprehensive process solutions, improvements and procedural changes to improve business process performance, process performance, productivity and efficiency. Present findings to group and clients.
  • Use Project Management tools and techniques to plan and track multiple operations.
  • Keep abreast of the newest developments/technologies; develop strategy and business plans for the implementation of appropriate platform technologies to improve infrastructure and throughput of media and process development, including high throughput cell culture systems.


Education and Experience:


  • MS or PhD in Biochemical Engineering, Cell Biology or related field
  • Minimum of 5 years of research experience in industry with strong track record in leadership and people management experience to motivate and maintain high performance from team
  • Experience and working knowledge of transient expression of proteins in mammalian (HEK, CHO) and baculovirus, E.coli, yeast fermentations and their subsequent characterization
  • Experience necessary to manage the Protein Expression Core including fermentation/bacterial, baculoviral/insect cell, and mammalian protein expression systems
  • Strong experience expressing secreted, soluble and membrane proteins on both the small and large scale (10L+)
  • Ability to develop methods for high yield expression of novel target proteins and the ability to perform and design complex experiments
  • Ability to plan tasks in the pipeline and be able to perform under aggressive delivery timelines

Excellent attention to detail as well as strong verbal and written comm

Our Bedford, MA facility has an opening for an entry-level Research Associate in our Protein Expression Core.  The successful candidate will be an individual who can perform laboratory activities with some supervision and who can also collaborate and coordinate within the group and across other core lab functions.  The successful candidate will be energetic, efficient and someone who thrives in a fast-paced environment.


  • Recombinant protein expression and analysis experiments using bacterial, insect and mammalian expression systems
  • Carry out multiple experiments in parallel and keep detailed, meticulous notes
  • Support and collaborate with core members and project managers
  • Preparation of stocks and other reagents
  • Analyze and report experimental results, both in daily updates and in final reports

Education and Experience:

  • BS / BA in related field
  • 1-2 years of applicable research experience
  • Laboratory skills in protein expression for a variety of proteins and expression cell types
  • Hands on expertise in molecular biology, protein expression an analysis and small scale protein purification is a plus


The primary role for this Business Development Manager will be to assist in lead generation, convert leads to proposals, and work with the broader team to win business in the greater San Francisco area.   Long term success will be heavily dependent on converting new clients to long-term partners.  Accordingly, the BD Manager will create and maintain strong relationships with key accounts in pharma and biotech.  The position will provide opportunities for direct selling to targeted accounts, relationship management and entrepreneurial marketing and promotion.



  • Both a life science and business degree (MSc or PhD in biological sciences and MBA) a plus
  • 8 years of sales history in the pharmaceutical/biotechnology industry with a proven track record
  • Comprehensive list of target clientele in the greater San Francisco area
  • Strong sales acumen and the ability to use a consultative selling approach
  • Demonstrated relationship building, listening and influence skills
  • Entrepreneurial spirit and a pro-active hands-on attitude
  • Willing to work in a dynamic environment and to learn from the team
  • Excellent verbal and written, strong presentation, analytical, organizational and interpersonal skills
  • Salesforce CRM, PowerPoint, Excel and other standard MS Office skills


We offer you a dynamic opportunity in an entrepreneurial business development atmosphere. You profit from an open and flexible company structure where initiative is appreciated and encouraged. The compensation and benefits package is competitive including base salary plus a variable commission based on successful closure of business opportunities directed at key performance indicators as defined by the Sr. Management team.


We have an opening for a Group Leader I in our Functional Biology Core Lab.  The primary responsibility of this position will be to manage the Functional Biology group successfully while also executing project related activities.  The successful candidate will be able to perform all Core duties in an independent fashion and will collaborate and coordinate within the group and across other Core lab functions.  The Group Leader I should be a critical scientific thinker and will be expected to perform experiments, analysis and troubleshooting, participate in project meetings and collaborate with Project Managers to determine the path forward for experiments.  The successful candidate will be energetic, efficient and thrive in a high paced environment.  The Group Leader I is expected to mentor, develop and lead all Functional Biology Core Lab scientists and to build strong relationships within the Core.  Superior communication skills are essential.


Primary Responsibilities:

  • Responsible for all Functional Biology Core Lab operational resource planning and organization of all request needs.
  • Extensive experience with experimental design and execution and to work collaboratively with junior and senior scientists.
  • Responsible for development and management of all Functional Biology Core Lab personnel including administrative tasks.
  • Execution of bench work to support all Functional Biology activities including but not limited to cell culture and cell engineering, execution of both in vitro functional cell based assays, biochemical characterization as well as phenotypic characterization. Assay development, optimization, analysis and interpretation skills are paramount.  Experience in high content analysis, cell biology and biochemistry is essential.  Phenotypic drug discovery experience is preferred.
  • Ability to maintain a quality system of record keeping and reporting in line with current practices.
  • Lead technical and procedural innovation within the Functional Biology group.


Education and Experience:

  • PhD with experience in a commercial setting preferred.
  • At least 8-10 years of applicable research experience.
  • Prior supervisory and management experience.
  • Extensive knowledge and experience with culturing and maintaining different cell lines simultaneously ranging from primary cell lines to stable cell lines.
  • Working knowledge with IncuCyte system, InCell Analyzer, MagPix Typhoon, Guava easyCyte, SpectraMax, LightCycler, Envision Plate Reader System, Tecan and high throughput automation.
  • Knowledge and understanding of recombinant protein biochemistry highly desirable.



Recorded on: Tuesday, January 24, 2017
Duration: 60 minutes
Featured Speaker: Douglas R. Davies, Senior Manager of Structural Biology, Beryllium Discovery Corp.

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This webinar will discuss the use of ligand-observe NMR techniques for rapid and efficient fragment screening of viral targets. Fragment screening was performed on two different viral proteins, an H1N1 Influenza A virus polymerase acid protein C-terminal domain (PA-CTD) and the Ebola virus matrix protein VP30 as part of a structural genomics consortium which targets infectious diseases. The influenza virus PA-CTD is part of the heterotrimeric viral RNA-dependent RNA polymerase involved in genome replication, whereas the Ebola virus VP30 protein is a phosphoprotein which associates with the nucleocapsid protein and is essential for viral transcription initiation.

In each case, the strategy was to target a protein-protein interface rather than an enzymatic active site. Interestingly, the majority of hits for the influenza A virus PA-CTD screen bind to a surface exposed site located near the viral RNA loading site rather than the expected PB1 N-terminus binding site which is a computational hot spot. Crystal structures of initial hits and follow on analogue-by-catalogue compounds were obtained. For the Ebola virus VP30 screen, VP30 was screened from both the 2013-2015 Zaire outbreak as well as the related Marburg virus VP30 in an effort to identify fragments which can target divergent viral VP30 strains. All of this work has been done as part of the Seattle Structural Genomics Center for Infectious Disease (SSGCID), a structural genomics consortium funded by the National Institute for Allergy and Infectious Diseases (NIAID).

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Doug Davies Senior Manager Structural BiologyAbout Douglas R. Davies, Senior Manager of Structural Biology, Beryllium Discovery Corp.
Over the past twenty years, some of Douglas’ work has focused on structural studies of functional nucleic acids and nucleic-acid modifying enzymes. His graduate thesis work at the University of Wisconsin-Madison involved the first structures of Tn5transposase. As a postdoctoral fellow at the University of Washington, Douglas studied the DNA repair enzyme Tyrosyl DNA Phosphodiersterase (Tdp1), elucidating the first crystal structures and verifying the proposed mechanism of action. During the past 10 years at Beryllium, he has applied these experiences to a number of DNA aptamer diagnostics and potential therapeutics (SOMAmers) as well as DNA Polymerase C from Geobacillus kaustophilus. Douglas is the lead crystallographer for 77 crystal structures in the Protein Data Bank and has published 28 peer-reviewed journal articles.



Ebolaviruses can cause severe haemorrhagic fever and was responsible for the 2013-2015 epidemic in West Africa, that resulted in over 11,000 deaths. Utilizing our fragments library, we employed saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy to identify fragments that bound Filoviridae family members, Ebolavirus Zaire or Marburgvirus Lake Victoria nucleoprotein transcriptional cofactor VP30. Due to the adaptive tendencies of viral proteins, we identified fragments that bound one or both strains. To further interrogate the potential relationship of fragments with Ebola, additional STD NMR screening of Ebolavirus Zaire mutants was performed, determining the difference signal of select fragments with the active “unphosphorylated” and inactive “phosphorylated” mutants. A greater difference signal was observed with the active mutant which also included the Marburgvirus specific fragments. We believe that our findings and strategy lead towards a structure guided drug design path for more successful viral therapies in Ebola and can be applied to other pathogens.

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Probing Filoviridae: Identifying fragments that bind Ebolavirus and Marburgvirus

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